PayPal is one of the most widely recognized digital payment systems, used by over 36 million merchants as of 2025. 

However, many Managed Service Providers (MSPs) discover that PayPal’s convenience comes at a cost. High credit card processing fees, limited MSP-specific integration capabilities, and generic billing workflows can become stumbling blocks for a growing MSP. 

PayPal’s platform is also designed for a broad audience. This means it often lacks features that MSPs require for their specialized client contracts, internal billing workflows, and recurring services.

MSPs reading this article are likely exploring better options. Here, we will highlight why MSPs are seeking PayPal alternatives and what key features to look for in a new billing solution. 

We’ll compare leading payment platforms side by side and explain why a purpose-built MSP payment tool, like FlexPoint, can address PayPal’s shortcomings. 

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Why MSPs Are Looking for PayPal Alternatives

Many MSP owners and finance teams eventually outgrow PayPal due to persistent issues with using it for client billing. 

Several common frustrations drive MSPs to seek alternatives:

• High Transaction Fees: PayPal charges up to 3.49% + $0.49 per transaction, which can significantly impact profit margins for MSPs handling large or recurring invoices. 
• Limited PSA/Accounting Integrations: PayPal does not natively integrate with specific PSA tools, such as ConnectWise or Autotask. This creates manual work and increases the risk of reconciliation errors.
• Generic Billing Workflows: PayPal lacks MSP-focused features such as recurring billing tied to contracts, credit card surcharging, and approval workflows.
• Basic Client Experience: With PayPal, your clients are redirected to PayPal’s website and interface to complete payment, rather than staying in a portal branded with your company's logo. Clients may encounter PayPal logos or offers (such as PayPal Credit) during checkout, which can be confusing and detract from your brand’s professionalism. 

In one MSP’s (IT Vortex) experience, using PayPal meant clients had to leave the MSP’s site and pay on a PayPal page. Transactions showed up under PayPal’s name, which some clients even mistook for fraud. 

• Payment Holds and Cash Flow Uncertainty: PayPal may freeze funds if it detects irregular activity. This delays deposits and disrupts operations. These unpredictable holds make it difficult for MSPs to maintain consistent cash flow.
• Security and Control Limits: While PayPal offers standard protections, it lacks features like MSP-specific compliance reporting. Support is generalized and not tailored to MSP billing needs.

Due to the issues mentioned above (high fees, weak integrations, unbranded experience, and unpredictable holds), many MSPs decide it’s time to switch. MSPs recognize that continuing to use a generic platform will hinder their growth and client satisfaction

8 Key Features to Prioritize in a PayPal Alternative for MSPs

When evaluating alternatives, MSPs should seek payment solutions that directly address PayPal’s weaknesses. 

Here are the must-have features and capabilities to prioritize in a new billing platform:

1. Deep PSA and Accounting Integrations:

For MSPs, syncing payment data with PSA software (such as ConnectWise, Autotask, HaloPSA, SuperOps) or accounting tools (such as QuickBooks Online, QuickBooks Desktop, Xero) is essential. 

A good payment gateway/platform should support real-time two-way syncing so invoices and payments update automatically across your PSA and accounting software. 

This eliminates manual data entry, saves hours of reconciliation work, and reduces the risk of billing errors.

2. Automated Billing and Payment Workflows:

Look for tools that automate recurring invoices, send payment reminders, expedite payment collection, and offer multiple payment methods (such as ACH/credit cards, installment plans, etc.). MSP billing is complex, and automation significantly reduces administrative time spent on tasks. 

One MSP, IT Vortex, saved over $15,000 per month by automating its billing and reconciliation processes. With less manual tracking, your team can focus on service, not collections.

3. Branded, White-Label Client Portals:

A fully branded client payment portal fosters trust by keeping clients within your environment, rather than directing them to external platforms like PayPal. Clients see your name, logo, and domain, not third-party offers or branding. 

User-friendly features, such as passwordless login and one-click payments, further enhance on-time collections and client satisfaction.

4. Flexible Payment Methods:

ACH payments are ideal for large invoices, with some platforms charging a flat fee averaging between $0.25 and $1.00 per transaction (with FlexPoint). 

A billing software that provides support for ACH (including Same-Day ACH), credit cards, AutoPay, and flexible financing provides your clients with options. 

With recurring and one-time payments handled in one place, you enhance your cash flow and reduce reliance on external tools.

5. Transparent, Cost-Effective Pricing:

Select a billing platform provider with transparent pricing and no hidden costs. If you process a high volume of credit card payments, choose a platform that allows you to pass on card processing fees using a transparent surcharge model. 

(Note: Credit card surcharging is not permitted in all U.S. states, so do your research before implementing this practice.)

Avoid platforms that surprise you with monthly charges or withheld funds. Always review the full fee schedule before committing.

6. Comprehensive Reporting and Analytics:

Strong reporting tools enable MSPs to monitor accounts receivable in real-time. Look for features like aging reports, DSO tracking, and daily deposit logs. Segmenting by client or service makes it easier to follow up and improve collections. 

As Atradius reports, over 50% of late payments are never collected, so proactive reporting is key.

7. Security and Compliance:

Select a provider that prioritizes compliance to safeguard client data and ensure adherence to regulatory requirements.

The platform should meet PCI DSS Level 1 standards and SAQ-A compliance, utilizing encryption, audit logs, and role-based permissions. 

FlexPoint, for example, uses passwordless PIN logins and ensures robust credit card data security. 

8. Dedicated MSP Support:

Look for a team that understands MSP billing workflows and offers client onboarding help, not just software access. The right vendor will assist with setup, data migration, and even client communication during the switch. 

Fast, knowledgeable support helps your MSP achieve faster results and avoid billing disruptions and payment friction.

In the next section, we’ll examine some of the top alternatives that meet these criteria and compare them.

5 Top PayPal Alternatives for MSP Billing and Payments

Now, let’s explore some of the leading PayPal alternative platforms and how they align with MSP requirements. Each of these options improves on PayPal in its own unique way. 

We’ll provide an overview of their pros, cons, pricing, and what makes them stand out from other platforms:

1. FlexPoint

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FlexPoint is specifically designed for MSPs, offering deep integration with tools such as ConnectWise, Autotask, HaloPSA, QuickBooks (both online and desktop versions), and Xero. Invoices and payments sync in real-time across all platforms, thus eliminating the need for manual reconciliation.

FlexPoint Features:

• Full billing cycle automation from PSA to accounting
• AutoPay for recurring service charges
• White-labeled client portal hosted on your domain
• Supports credit cards, ACH, same-day ACH, and client financing/installment plans (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 across all connected platforms
• 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:

• Limited integrations beyond PSA and accounting (but expanding soon based on MSP/customer feedback)

FlexPoint Pricing:

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

2. Stripe + Custom Portal

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‍Stripe is a popular payment processor known for its flexibility and developer-friendly tools. For MSPs, Stripe can serve as a PayPal alternative by providing support for ACH bank transfers, credit/debit cards, and digital wallets, such as Apple Pay. 

However, Stripe by itself is just a backend processor: MSPs would typically need to build or use a custom client portal or integration (through APIs or third-party tools) to link Stripe with their PSA or to provide a branded payment experience.

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:

• Multiple payment methods such as credit cards, ACH, and digital wallets
• Fraud protection tools like Stripe Radar

Cons of Using Stripe:

• Requires development effort to create a branded client experience
• Not MSP-specific; no native ConnectWise or Autotask integration
• 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

3. Maxio (previously Chargify)

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Chargify, now rebranded as Maxio, is a subscription billing platform built for SaaS companies. MSPs offering usage-based or packaged recurring services may benefit from its advanced automation and analytics, though traditional MSP models may require customization.

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 smaller MSPs
• Requires a separate payment gateway for processing

Maxio Pricing:

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

4. GoCardless

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GoCardless is a payment platform focused on ACH and direct debit transactions. It’s ideal for MSPs with recurring contracts who want to reduce credit card fees by pulling payments directly from client bank accounts. While not an all-in-one solution, it pairs well with existing invoicing or portal tools.

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, since they primarily focus on ACH/debit-only transactions
• 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

5. Stax Payments (Fattmerchant)

Stax Payments offers a flat-fee subscription model that can significantly lower costs for MSPs with high monthly billing volume. Unlike PayPal, which charges a percentage of each transaction, Stax passes through interchange rates and offers all core payment tools in one system.

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 Delivers More for MSPs Than PayPal

These five alternatives (FlexPoint, Stripe, Chargify, GoCardless, Stax) each offer distinct benefits beyond what PayPal can do for an MSP. 

However, among the alternatives discussed, FlexPoint stands out as the platform specifically built to address MSPs’ challenges with PayPal. 

Let’s detail how FlexPoint solves the pain points we outlined earlier and delivers a superior experience tailored to MSPs:

1. Purpose-Built for MSPs:

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FlexPoint is designed to align with the way MSPs operate their billing workflows. This means it supports contract-based recurring billing, one-off project invoices, and even automatic compliant surcharging for credit card fees (where permitted). 

PayPal’s generic approach can’t match this specialization. With FlexPoint, if your client agreement includes a monthly fixed fee and occasional overage charges, the system can handle both seamlessly. 

The platform can automatically add late fees or percentage-based fees if you choose, reflecting standard MSP practices (like charging 3% for credit card use to offset costs). 

In PayPal, you would have to manually figure out and add those charges, if it’s even allowed. Essentially, FlexPoint automates the entire payment cycle for MSP services, whereas PayPal would require you to do a lot of manual work.

2. Deep PSA & Accounting Integrations:

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With PayPal, you would have to manually mark the ConnectWise invoice paid and reconcile the transaction in QuickBooks yourself. FlexPoint’s integration not only saves time but also reduces billing errors. No more forgetting to update a system or mistyping an amount. 

According to survey data from Ledge’s month-end close benchmarks for 2025, finance teams spend, on average, 20-50 hours per month on manual cash reconciliation. 

Considering the time investment, even a small MSP finance team could be losing 240 to 600 hours per year on reconciliation alone. That doesn’t account for the added cost of errors, delayed reporting, or missed revenue from untracked payments. For MSPs trying to grow or maintain profitability, those inefficiencies add up quickly.

Unlike PayPal, FlexPoint offers out-of-the-box integration with the key software MSPs use. The platform connects directly with PSA systems (such as ConnectWise, Autotask, SuperOps, HaloPSA) and accounting platforms (including QuickBooks Online, QuickBooks Desktop, and Xero). 

FlexPoint’s GL Connect takes data syncing a step further with two-way sync between ConnectWise PSA and QuickBooks Online.

For example, suppose a client pays through FlexPoint’s client portal. In that case, that payment record will automatically appear in ConnectWise (marking the invoice as paid) and in QuickBooks (logging the payment and reconciling the associated deposit automatically)

This gives MSPs confidence that their financial data is consistent across all platforms. PayPal’s limited integration (essentially just exporting data or using third-party sync tools) can’t match the reliability of FlexPoint.

3. Branded Client Experience:

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FlexPoint allows MSPs to present a fully branded payments portal to clients. Your clients log in to ‘Your MSP Payments’ on your website, not a PayPal page. They see your logo, your professional branding, and a modern and simple interface. The portal enables them to view all their invoices, pay online, set up automatic payments, or even securely set up and allow multiple payment methods. 

Clients are left feeling like they’re interacting with a professional white-label billing system that you’ve provided for their convenience. This dramatically increases trust. Many MSPs (such as TAZ Networks, IT Vortex, Circuit Saviors) find that after switching to FlexPoint, clients pay faster and have fewer questions, because the process is transparent and on-brand. 

Compare this to PayPal, where clients might be unsure (“Do I need a PayPal account?”, “Why am I on PayPal’s site? ") and sometimes hesitate or delay payment. 

Additionally, FlexPoint’s emails (including invoice notifications and receipts) originate from your email address or domain, not a PayPal address, which maintains consistency in communication and prevents essential messages from being overlooked. 

In short, FlexPoint helps MSPs deliver a smooth, company-branded payment experience, which reflects well on your MSP.

4. Comprehensive Payment Flexibility:

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FlexPoint combines the best of both worlds in terms of payment methods. The platform enables you to accept credit cards and ACH. 

In addition, FlexPoint also supports partial payments and installment plans if needed (useful for large projects with milestones). 

This payment flexibility allows you to offer your clients multiple ways to pay their invoices. 

Suppose your MSP is handling a $12,000 server upgrade project. You’ve agreed with the client to bill in three stages: 40% upfront, 40% after hardware delivery, and 20% on final install.

With FlexPoint, you can break this into three scheduled payments:

• $4,800 due immediately
• $4,800 due on the delivery date
• $2,400 due on completion

Each payment can have its own method, surcharge setting, and AutoPay rule. The client may pay the first two installments by credit card (with a 3% surcharge applied) and the final balance via ACH to avoid additional fees.

You don’t need to manually create three invoices or track reminders. FlexPoint manages the schedule, notifies the client before each due date, and processes the payments automatically according to your settings.

This type of control is not possible in PayPal, where invoices are typically one-time, full-balance requests without automation or rule-based logic. FlexPoint provides both flexibility and automation, enabling you to structure payment terms in a way that suits your service model and preserves your margin.

Critically, it also has a built-in surcharge feature for credit card payments: if you choose, you can automatically add, for example, a 3% fee for clients who pay by card, to recover the processing costs. This is configured in compliance with legal state-specific rules and shown transparently to the client at checkout (so there are no surprises). 

PayPal does not offer automatic surcharging and, in fact, historically discourages it. With FlexPoint, you have the flexibility to either pass on or absorb credit card processing fees at your discretion for each client or invoice. 

FlexPoint also supports Same-Day ACH, giving you even more control over cash flow, instead of waiting a few days for standard ACH deposits. Same-Day ACH means funds can reach your account on the same business day. This makes a considerable difference when you're managing payroll, vendor payments, or urgent project expenses, especially at month-end when cash flow timing matters most.

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You can also configure AutoPay rules on a client-by-client basis. For instance, you can set all clients on agreement X to be auto-charged monthly, and FlexPoint will handle it.  

Clients also appreciate options: those who prefer ACH payments can do so (saving you money), and those who insist on cards can use them (with you deciding how to handle the fee). Everyone wins compared to PayPal’s relatively rigid system.

5. Transparent, Lower Fees:

FlexPoint’s fee structure is transparent. As mentioned, ACH transactions are very low cost, and card fees are competitive and flat (and can be surcharged). There are no fees to send invoices, no monthly account fee for standard features, and no sudden rate hikes. 

PayPal, on the other hand, has been known to raise rates or introduce new fees (like the $20 chargeback fee, higher international rates, etc.). Moreover, PayPal can hold your funds without warning, effectively costing you money if you can’t access revenue when needed. FlexPoint does not randomly hold your money. 

As long as the payments are legitimate and clear the banks, you will receive your deposit within the stated time frame (which can be next-day for cards and as fast as same-day for ACH). 

This reliability is crucial. 

MSPs have reported saving significant amounts after switching to FlexPoint, not just from lower fees, but also from improved cash flow and reduced losses. 

For example, as noted in an earlier section, IT Vortex, an NJ-based MSP, achieved savings of over $ 15,000 per month on billing costs and a reduction of 30 days in payment cycles by using FlexPoint. 

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Such results demonstrate how a transparent and efficient system like FlexPoint can directly benefit an MSP’s bottom line.

6. Fast Onboarding and MSP-Centric Support:

Transitioning from PayPal to a new system might sound daunting, but FlexPoint makes it as painless as possible. 

For example, guided onboarding helps you import your client list, set up integrations, and tailor the portal to your branding. You can even receive templates to notify clients about the change, emphasizing the benefits for them (like a more convenient portal). 

The FlexPoint onboarding process is broken into four phases. Within each phase, the onboarding process takes you through multiple steps, including everything from account creation right up to going live. 

Because FlexPoint’s team works closely with MSPs every day, they can anticipate questions and offer best practices during the setup process. This contrasts with PayPal, where you’re basically on your own to figure out how to make it work for your MSP. 

Post-launch, if an issue arises (such as a client’s payment not going through or you need to configure a new integration), FlexPoint’s support is readily available and understands the urgency of billing issues.

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Many MSPs feel like they have a partner in FlexPoint, not just a vendor. That kind of relationship means you get more value over time. As your MSP grows or changes, FlexPoint can advise on how to adjust your billing processes accordingly. 

With PayPal, by comparison, you’re unlikely to ever speak to someone in support who understands what an MSP even is, let alone how to optimize billing for one.

7. Real-Time Reporting:

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Finally, FlexPoint provides a rich set of reports tailored to MSP finance needs. 

PayPal’s reporting is quite basic: you can view transactions, but it’s not designed to provide aging reports or integrate with contract terms. With FlexPoint, because it is aware of your agreements and invoices, it can automatically produce useful metrics. 

It basically becomes your A/R command center. This means fewer spreadsheet exports and manual consolidations for you. Instead, you have up-to-date information to drive decisions (like maybe increasing a client’s credit limit or focusing collection efforts on a specific aging bucket).

In summary, FlexPoint addresses every major reason MSPs grow frustrated with PayPal. It’s an MSP-focused solution that brings automation, integration, and cost savings all under your control. FlexPoint doesn’t just replace PayPal; it upgrades your whole billing process into something more efficient and scalable. 

Conclusion: Choose a Billing Platform Built for MSPs

In the middle of managing clients, tickets, and technology, MSP leaders & owners shouldn’t have to battle their payment platform. If PayPal’s fees, limitations, and generic setup have been holding back your billing, it’s time to consider an upgrade. 

The right payment solution will:

• Streamline your entire billing and payments workflow
• Improve your client’s payment experience
• Scale with your MSP’s growth

As we’ve seen, there are several strong options out there, from flexible toolkits like Stripe to specialized services like GoCardless. 

However, many forward-thinking MSPs are gravitating toward platforms purpose-built for their industry, as these tend to deliver the most significant efficiency gains.

FlexPoint stands out as an ideal choice for MSPs ready to elevate their billing and payments. It combines automation, integration, and cost-effectiveness in a package designed specifically for the MSP business model. 

For example, Pileus Technologies, a growing MSP, implemented FlexPoint to improve collection efficiency and offer financing to prospective clients. Following integration, the company reported an 80% reduction in payment processing time and a 5% increase in new customer acquisition, which was attributed to FlexPoint’s financing capabilities.

According to President John Douglass, the automation provided by FlexPoint significantly reduced administrative workload, allowing the team to remain focused on operational growth.

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Moving away from PayPal can be a pivotal step in professionalizing and scaling your MSP’s finance operations. Don’t settle for a system that wasn’t built with your MSP’s specific needs in mind. 

Tired of PayPal’s fees and limited features? 

FlexPoint is built for MSPs, with powerful automation, seamless integrations, and branded payment experiences.

Schedule a demo to see how FlexPoint can upgrade your billing and payments.

Additional FAQs: PayPal Alternatives for MSPs

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