According to data from MSP Insights, 70% of MSPs struggle with cash flow issues, a problem often linked to outdated or inefficient billing processes. That number underscores how important it is for managed service providers (MSPs) to regularly revisit and refine their billing systems.

For many, WisePay has been a trusted tool for processing client payments and integrating with the ConnectWise ecosystem. It’s helped MSPs manage invoicing and collections as they’ve grown. 

Over time, however, some MSPs find their needs extend beyond what WisePay was built to deliver. As service offerings expand and client expectations rise, features like advanced billing automation, broader payment options, and a branded client experience become increasingly valuable.

If a platform like WisePay cannot deliver in these areas, it’s time to consider alternatives that can. Upgrading your billing system can be an opportunity to save time and boost efficiency in your finance workflows. Consider it a strategic upgrade.

In this article, we will outline what to look for in a WisePay replacement, compare top alternatives, and explain how a purpose-built MSP payment solution like FlexPoint can support both operational efficiency and long-term growth.

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Why MSPs Seek Alternatives to WisePay

Several challenges with WisePay have driven MSPs to explore other options.

For example, one common frustration is the onboarding process. 

Setting up WisePay involves multiple steps and a lengthy merchant account application process, which can delay your start and create additional work. For an MSP eager to improve billing quickly, this slow implementation is a serious drawback. 

Many report needing a lot of support just to get WisePay configured correctly. This isn’t ideal when you want a relatively ready-made solution that provides quicker onboarding for both you and your clients..

Another limitation is automation and transaction visibility. WisePay offers only basic payment tools, so tracking invoice statuses and payments end-to-end isn’t always easy. Users have noted difficulty seeing what’s been paid or synced at a glance. 

There’s also no automatic deposit reconciliation. A member of the MSP finance/accounting team has to manually match payments with bank deposits, which consumes valuable time. These gaps can lead to confusion and administrative delays when your team is trying to reconcile accounts or chase down unpaid invoices.

Client experience is another area where MSPs outgrow WisePay. The platform’s client portal is functional but dated. WisePay lacks features such as branded payment portals and email tracking.

In practice, clients might receive invoices from a generic email or portal that isn’t tied to your MSP, leading to confusion. A smooth, branded payment experience matters for professionalism and client trust. For many MSPs, WisePay doesn’t fully deliver on that front.

MSPs have also cited support and flexibility issues. As a ConnectWise-owned product, WisePay often comes bundled with long-term contracts (usually one to three years). This means you’re locked in even if the tool isn’t meeting expectations. 

Switching platforms mid-contract (usually 1 to 3 years) can be costly or impossible, leaving growing MSPs stuck with limitations. Additionally, WisePay only integrates with two PSA tools: ConnectWise PSA and Datto Autotask PSA.

Even within ConnectWise, some users describe the workflow as fragmented, as they juggle multiple portals for PSA, quoting, and payments. All of this adds up to added complexity that busy MSP teams don’t need.

If you’re one of the many MSPs whose tech stack consists of ConnectWise and QuickBooks Online, then you also know the fact that you need yet another solution – Wise-sync – to sync data across both platforms. Although Wise-Sync is now commonly a part of WisePay, it’s still a single-use sync tool with major limitations. There are alternatives to sync across ConnectWise and QuickBooks Online, though.

Finally, many MSPs simply outgrow WisePay's feature set. As your operation scales, you may require advanced capabilities that WisePay lacks. 

When MSPs hit these roadblocks, it becomes clear that sticking with the status quo could hold the business back. In a competitive MSP industry, efficient billing and timely payments are essential for healthy growth and client satisfaction. That’s why so many MSP owners start looking for a better alternative.

6 Key Features to Look for in a WisePay Alternative

When you’re evaluating an alternative payment system to WisePay, it’s important to know which features will make the biggest difference for your MSP. 

Below is a checklist of key capabilities to prioritize in any WisePay alternative:

1. Deep PSA Integration

Select a platform that integrates seamlessly with your PSA software (e.g., ConnectWise, SuperOps, Autotask, HaloPSA) and your accounting software (e.g., QuickBooks Online, QuickBooks Desktop, Xero). This ensures invoices, payments, and client data flow automatically between systems. Smooth integration prevents data entry errors and keeps your financial information up-to-date with minimal effort. 

For example, when your PSA creates an invoice, the billing platform should pull the data in, process the payment, and mark it as paid in QuickBooks without manual steps.

Use both ConnectWise and QuickBooks Online? Look for a tool with a dedicated two-way sync to ensure cleaner data in real-time.

2. Advanced Automation

Look for tools that automate repetitive billing tasks. According to data from Amalto Technologies, 61% of late invoice payments occur due to invoice errors.  Automating repetitive billing tasks reduces the risk of errors, shortens payment cycles, and ensures invoices and reminders are sent on time and consistently. This consistency improves cash flow and helps prevent overlooked payments. 

The right billing solution will automatically send invoices on schedule, remind clients about upcoming or late payments, and even handle retrying failed payments. 

Automation should also cover things such as recurring billing for managed services and auto-collecting payments (AutoPay) under rules you define. 

By cutting out manual billing work, you free up your team’s time and reduce human error. MSPs leveraging payment automation have seen substantial improvements.

For example, Pileus Technologies, a Kansas-based MSP, reduced payment processing times by 80% after switching to an MSP-specific payment platform, FlexPoint. With automated invoice collection and accounting software sync, their finance team now spends far less time chasing payments or logging transactions manually.

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3. Branded Client Portals

A professional, easy-to-use payment portal is a must. This feature creates a smoother payment experience for clients and strengthens their confidence in your MSP. 

Your clients should be able to click a link and access a branded portal (with your company logo and colors, ideally on your own domain) where they can view invoices, save multiple payment methods, and make payments securely. 

A robust payment portal will show clients current and past invoices, so they have complete transparency on all their payment and billing activity with you. 

The platform should also support self-service, enabling clients to onboard seamlessly and update their billing information or enroll in AutoPay independently. This improves the client experience and reduces back-and-forth for your team. 

Crucially, a branded portal reinforces your MSP’s identity (not the software vendor’s), which helps build trust between you and the clients you serve.

4. Multi-Method Payment Support

Your new platform should give clients flexible ways to pay. Flexible payment options like “Buy Now, Pay Later” are gaining traction. The global BNPL market reached $340 billion in 2024, and it continues to grow. 

Further, businesses using BNPL report distinct advantages. For example, according to data from Allianz-Trade, merchants offering BNPL options have seen up to a 40% increase in conversion rate.

However, not all billing platforms offer native support for payment/installment plans. A platform that enables structured, automated payment plans allows you to split larger invoices into manageable installments. 

This can reduce client resistance to high upfront project costs, improve cash flow predictability, and increase close rates on high-ticket services.

Without built-in payment plan functionality, MSPs must either manage installment schedules manually or seek out third-party financing tools. These workarounds increase complexity and administrative burden. 

In contrast, platforms like FlexPoint provide built-in controls for defining payment terms, automating due dates, and sending reminders, making it easier to offer flexible arrangements without extra tools or labor.

At a minimum, your payment options should include accepting credit/debit cards and ACH (bank transfers). Ideally, your payment platform can also handle other methods, such as electronic checks or even digital wallet payments.

For MSPs that manage projects, hardware rollouts, or onboarding phases, payment plans provide a more accommodating experience for clients and a more efficient billing process for internal teams.

Credit card surcharging support is also important for many MSPs. This feature allows you to automatically add a processing fee for credit card transactions (in states permitted by law) so that you can pass through or recoup those costs. 

Not all payment platforms allow surcharges. However, it’s a valuable option to have, as it can save your MSP thousands in processing fees over the year. 

5. Robust Reporting and Visibility

Replacing WisePay is a chance to gain a deeper understanding of your billing operations. Choose a platform with real-time reporting dashboards, detailed financial reports, and payment analytics. 

For example, you should be able to view totals for paid versus outstanding invoices quickly, your daily cash receipts, and key metrics such as Days Sales Outstanding (DSO). 

The billing solution you choose should notify you (and integrate with your PSA) when a payment fails or an invoice is overdue, so nothing falls through the cracks. 

Comprehensive reporting helps you spot trends (such as slow-paying clients or rising credit card fees) and make informed decisions. This feature also makes month-end reconciliation easier by clearly matching payments to invoices and deposits.

6. Scalability and Support

Finally, pick a billing solution that will grow with your MSP and back you up when you need help. 

“Scalability” in this context means the platform can handle an increasing volume of invoices and payments reliably without performance issues. It also means that the platform offers features (or higher-tier plans) to support more complex needs as you expand. You don’t want to switch again in a year or two because you’ve outgrown the software. 

Additionally, consider the vendor’s customer support and training offerings. 

MSP-focused billing solution providers will understand your use case and offer responsive support, whether that’s live chat, a dedicated rep, or an extensive knowledge base. Quick, knowledgeable support can be a lifesaver during onboarding or if an issue arises during billing. 

Check if the vendor offers onboarding assistance or data migration help, which can smooth the transition from WisePay to the new system.

Keep this feature checklist in mind as you evaluate alternatives. The goal is to address the shortcomings that pushed you away from WisePay in the first place. 

Suppose an option hits all these marks (smooth integration, strong automation, an outstanding client experience, flexible payments, insightful reporting, and room to grow). In that case, it’s likely to serve your MSP well for the long haul.

Top 5 WisePay Alternatives for MSP Billing

There are several platforms on the market that MSPs can consider when moving on from WisePay. 

Below, we’ve curated a list of top alternatives, each with a brief overview of how they stack up for MSP-specific billing needs. We’ll cover who each solution is best for, their key strengths, and any potential limitations in an MSP context.

1. FlexPoint

FlexPoint is a modern billing and payment automation platform built specifically for MSPs. It’s often seen as the most direct upgrade from WisePay, addressing many of its limitations. 

For growing MSPs seeking more control, automation, and integration, FlexPoint is a strong WisePay replacement built for long-term scalability.

FlexPoint Features:

• Full billing cycle automation from PSA software to accounting software
• Full sync capabilities across ConnectWise and QuickBooks Online, replacing Wise-Sync
• AutoPay for recurring service charges
• White-labeled client portal hosted on your domain
• Supports credit cards, ACH, same-day ACH, and client financing (FlexLine)
• Dashboards for A/R aging reports, DSO KPIs, and cash flow insights

FlexPoint Integrations:

• Syncs with accounting systems such as QuickBooks Online, QuickBooks Desktop, and Xero
• Syncs with MSP-specific PSAs: ConnectWise, Autotask, SuperOps, and HaloPSA

Pros of Using FlexPoint:

• Built for MSP workflows and billing models
• Eliminates deposit reconciliation errors through full system sync
• Branded client portal improves trust and payment speed
• Flexible payment options and financing features
• Option for MSPs to surcharge credit card transactions, but subject to state-specific surcharging laws
• Transparent pricing with responsive MSP-focused support

Cons of Using FlexPoint:

• No international payment processing, only USA at this time

FlexPoint Pricing:

• Scalable plans based on monthly processing volume
• ACH payments as low as $0.25
• Credit card fees are competitive
• No long-term contracts or hidden fees

2. Maxio (Formerly Chargify)

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Chargify, now rebranded as Maxio, is a subscription billing platform built for SaaS companies. The platform is well-suited to MSPs offering fixed-price service bundles or SaaS-style plans.

Maxio is a good option if your billing is fully productized. However, if you rely on time-based billing or require in-depth PSA integration, other solutions on this list may be a better fit.

Chargify (Maxio) Features:

• Consolidated invoicing across multiple services
• Proration and mid-cycle changes are handled automatically
• Built-in dunning tools for failed payments
• SaaS metrics dashboard for MRR (monthly recurring revenue), client churn, and LTV (customer lifetime value)

Maxio Integrations:

• Integrates with gateways like Stripe, PayPal Payflow, and Authorize.Net
• Syncs with QuickBooks, Xero, and Salesforce (via connectors)

Pros of Using Maxio:

• Detailed billing analytics and financial insights
• Consolidated invoicing simplifies billing for clients

Cons of Using Maxio:

• Not designed for ticket-based or hourly billing
• No native ConnectWise or Autotask integration
• It can be expensive for most MSPs
• Requires a separate payment gateway for processing

Maxio Pricing:

• Pricing starts at $599/month for up to $100k/month in billing

3. GoCardless

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GoCardless specializes in ACH and direct debit payments, pulling funds directly from clients’ bank accounts on a schedule. For MSPs focused on recurring billing, the platform offers a low-fee, automated way to collect payments without relying on credit cards.

GoCardless works well for MSPs whose clients are comfortable with ACH and who want to reduce card processing fees. If you need more payment options or a branded client portal, you’ll likely need to supplement it with other software.

GoCardless Features:

• Recurring ACH and international direct debit support
• Smart retry logic (Success+) to improve collection rates
• Email notifications for mandates, payment failures, and due dates

GoCardless Integrations:

• Integrates with QuickBooks, Xero, and Sage

Pros of Using GoCardless:

• Lower transaction costs than PayPal or credit card processors/payment gateways
• Supports international direct debit for global clients

Cons of Using GoCardless:

• No credit card payment support, ACH/debit only
• Lacks native PSA integrations (manual or API connection required)
• Client-facing tools are minimal, with limited branding options
• Slower funding times than card processors (2–5 business days)
• Transaction limits may apply for large invoices

GoCardless Pricing:

• Standard pricing begins at 0.5% + $0.05 per ACH transaction, capped at $5
• Advanced pricing starts at 0.75% + $0.05, capped at $6.25
• Pro pricing starts at 0.9% + $0.05, capped at $7
• International payments range from 1.5% to 1.9% + $0.05, depending on plan (no cap)
• Refunds cost $0.50, and chargebacks or failed payments are $5 each after 15 per month
• Custom pricing and add-ons (like branded statements and advanced API access) are available on request

4. Stripe + Custom Portal

Stripe is a flexible, developer-focused payment platform that MSPs sometimes pair with a custom-built portal to replace WisePay. The platform supports credit card, ACH, and digital wallet payments, along with recurring billing, automatic retries, and detailed reporting.

Stripe Features:

• Offers recurring billing tools through Stripe Billing
• Developer-friendly API for building branded portals or workflows
• Global payment support across many currencies and regions

Stripe Integrations:

• Native integrations with QuickBooks, Xero, NetSuite, and others

Pros of Using Stripe:

• Fraud protection tools like Stripe Radar
• Lower ACH fees for large transactions (capped at $5)

Cons of Using Stripe:

• Not MSP-specific; no native ConnectWise or Autotask integration
• Requires development effort to create a branded client experience
• Account holds can occur based on automated risk flags

Stripe Pricing:

• Credit card: 2.9% + $0.30 per transaction
• ACH: 0.8%, capped at $5
• Optional tools (like Stripe Billing) may have additional fees
• No setup or monthly base fee

5. Stax Payments (Fattmerchant)

Stax (formerly Fattmerchant) is an all-in-one platform that combines payment processing, invoicing, and recurring billing. Its subscription-style pricing model may benefit high-volume MSPs.

For MSPs looking for a generalist billing solution with flat-rate processing and basic automation, Stax can work. However, MSPs must be prepared to manage PSA integration manually and confirm whether its surcharging setup fits their needs.

Stax Features:

• Invoicing and recurring billing support
• Branded client payment portal with card and ACH support
• Real-time dashboard for transaction tracking and reporting

Stax Integrations:

• Integrates with QuickBooks Online and QuickBooks Desktop

Pros of Using Stax:

• Lower processing costs for high-volume MSPs
• Supports surcharging and cash discount programs

Cons of Using Stax:

• No native ConnectWise or Autotask integration
• Monthly fee may not be cost-effective for low-volume MSPs
• Limited international payment support
• The feature set isn’t tailored to MSP-specific workflows
• Interchange-plus pricing requires getting comfortable with variable rates

Stax Pricing:

• Starts at $99/month for up to $500,000/year in processing
• ACH typically costs $1 per transaction
• Interchange fees vary by card type; no added markup from Stax
• No long-term contracts or cancellation fees

How FlexPoint Stands Out as the Best WisePay Alternative for MSPs

All the alternatives above bring something to the table. However, FlexPoint distinguishes itself with a combination of MSP-tailored features and ease of use that’s hard to beat. 

Here’s how FlexPoint stands out as the top WisePay replacement:

1. Purpose-Built for MSP Billing

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FlexPoint isn’t a generic payment processor or billing solution. The platform is designed from the ground up for managed service providers. This means the platform understands MSP business models such as recurring service contracts, time-based billing, and project work. FlexPoint automates the entire ticket-to-invoice-to-payment cycle. 

For example, when a service ticket is closed or a milestone is reached, FlexPoint (through PSA integration) can trigger invoice creation, send it to the client, and even automatically charge the saved payment method on file if authorized. 

This level of automation, tailored to MSP workflows, goes well beyond what WisePay offers. Essentially, FlexPoint was created to fit how MSPs operate, so you won’t be bending your process to fit the tool; the tool fits your MSP.

2. Branded Client Portal

With FlexPoint, you get a fully white-labeled client payment portal that lives on your own domain. Your clients can log in to a unique, customized portal and see your branding while they manage their bills. 

The portal provides a clean, modern experience where clients can view all their invoices (past and present), choose payment methods, configure AutoPay, and add/remove portal users.

When it’s your brand front and center, clients feel as though they’re interacting directly with you, not a third-party system. This improves trust and makes it less confusing than the unbranded alternatives that clients might find puzzling. 

Moreover, the ease of use means fewer client hurdles in actually submitting payments, which leads to faster payments and fewer overdue invoices for you.

3. End-to-End Automation

FlexPoint automates the heavy lifting in billing. The platform can generate invoices from your PSA data, send them out on schedule, and handle the collection process without manual intervention. 

Clients can save a credit card or bank account and enroll in autopay, allowing their invoices to be paid automatically on due dates, eliminating the need to chase down payments. The system sends payment reminders and past-due notices according to rules you set, which keeps receivables in check. 

Importantly, FlexPoint includes automated deposit reconciliation, matching each payment to the deposit in your bank account and even syncing that back to your accounting software.  

The result is a near “set-and-forget” billing process: you set it up once, and then invoices go out and payments come in without constant oversight. 

Of course, you can always step in and take manual control when needed, but day-to-day, FlexPoint saves MSPs countless hours by automating routine tasks.

4. Flexible Payment Options

Many MSPs want more than just standard credit card and ACH processing. 

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FlexPoint expands payment flexibility with support for credit cards, ACH, Same-Day ACH, and client financing through FlexLine, all built into one platform. This enables MSPs to tailor payment terms to meet client needs without compromising cash flow.

Take a $12,500 infrastructure upgrade as an example. Instead of requesting the entire amount up front, FlexPoint allows you to set up a three-part schedule tied to project milestones.

This schedule could look as follows:

• $5,000 when the contract is signed
• $4,500 after hardware installation
• $3,000 following system testing and acceptance

Each stage can use a different payment method. A client might put the first payment on a corporate card for rewards, use ACH for the second to avoid processing fees, and send the final payment via Same-Day ACH for immediate clearance. 

Once the terms are set, FlexPoint manages the entire process: issuing invoices, sending reminders, applying surcharges when applicable, and collecting payments without requiring manual oversight from your team.

Same-Day ACH is beneficial for time-sensitive situations. These situations include covering vendor bills, funding payroll, or balancing month-end accounts. Instead of waiting the typical two to five days for standard ACH to clear, you can have funds in your account within hours.

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The platform also lets you define AutoPay rules by client, contract type, or even specific projects. This way, recurring service agreements can be charged automatically, while project work follows a milestone schedule. 

Clients benefit from flexible arrangements, and your MSP maintains consistent, predictable revenue.

5. Seamless MSP-Specific Integrations

FlexPoint integrates with a wide range of software that MSPs use. The platform integrates not just with ConnectWise, but also with Datto Autotask, HaloPSA, SuperOps, QuickBooks Online, QuickBooks Desktop, and Xero. 

Whether you’re a ConnectWise shop or not, FlexPoint can slot into your tech stack, which is a significant advantage over WisePay, which only really caters to ConnectWise and Autotask users.

Because FlexPoint is vendor-agnostic, you’re not locked into any single ecosystem. If you change PSA or accounting systems down the road, FlexPoint can likely integrate with the new one, so your payment process remains uninterrupted. 

Additionally, being independent (not owned by a PSA company), FlexPoint’s support team is focused on MSP payment issues, not general software support. You get MSP-centric customer service and ongoing improvements driven by MSP feedback. 

This integration depth and focus mean FlexPoint can truly centralize your billing. FlexPoint becomes the hub that connects tickets, invoices, payments, and accounting altogether in real time.

In short, FlexPoint stands out by offering an all-in-one platform that directly addresses WisePay's noted shortcomings. It’s faster to implement (you can be live in a day, not weeks), easier for clients to use, and far more automated.

Conclusion: Choose the Right Billing Solution for Your MSP

Switching away from WisePay is an opportunity to streamline your entire billing process and strengthen your business. The correct billing solution will save your team time, reduce errors, and get you paid faster. 

As you evaluate alternatives, keep your MSP’s specific needs front and center. 

Look for the features that will solve your current pain points: 

• Automation and data syncing to cut down on manual work
• Integrations to keep systems in sync
• Credit card surcharging to protect your margins
• ACH (even Same-Day ACH) for more cost-effective payment
• Flexible financing or installment plans to help acquire new clients
• A smooth client payment experience that makes it easy for clients to pay you

Also, consider the flexibility of each option, including contract terms and customization, to ensure the platform can adapt as your MSP grows.

In the end, the goal is to choose a platform that not only replaces WisePay but truly upgrades your capabilities. FlexPoint is the strongest contender here. The platform offers an all-in-one solution tailored to MSP workflows, eliminating many of the frustrations that WisePay users faced. 

MSPs that move to FlexPoint also often see measurable gains in efficiency and profitability. 

For example, Pro IT, a high-growth MSP in the American Northwest, upgraded from a legacy payments platform to address rising credit card fees and constant client troubleshooting requests.

Since making the switch, Pro IT has saved $70,000 per year, cut 160 hours of monthly admin work, and reduced the share of payments incurring credit card fees by 60%. 

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The combination of a user-friendly client portal, passwordless sign-in, and flexible payment options has simplified transactions for clients while freeing Pro IT’s team to focus on higher-value work.

These outcomes show how a platform like FlexPoint can turn billing from a resource drain into a profitable, scalable process.

Looking for a WisePay alternative built for modern MSPs? 

FlexPoint combines billing automation, PSA integration, and a branded client portal—everything you need to streamline payments and boost cash flow.

Schedule a demo to see FlexPoint in action

Additional FAQs: WisePay Alternatives for MSPs

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