As your MSP grows, so do your billing complexities. From managing recurring subscriptions to ensuring financial accuracy, the demands on billing processes can quickly become overwhelming. 

Common payment challenges, such as delays, errors, and missed payments, can erode revenue and client relationships. 

Relying on manual methods or fragmented systems is no longer an option. That’s why MSPs must select the best billing software to meet their needs. These automated tools streamline invoicing, accelerate payments, and provide real-time financial insights, enabling them to scale their operations while confidently maintaining top-notch client service.

This article explores the leading MSP billing solutions for 2025 and beyond. We discuss billing software designed for MSPs to simplify invoicing & billing, reduce manual effort, and strengthen your MSP’s financial health. 

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Why MSP Billing Software is Essential for Managed Service Providers

When handled manually, managing various billing scenarios, such as recurring subscriptions, various pricing models, and one-time project fees, can quickly become overwhelming. 

Manual invoicing often requires significant time and effort, increasing the likelihood of billing errors that can lead to billing disputes, delayed payments, and strained client relationships. 

Adopting an automated billing solution streamlines these processes, ensuring accuracy, saving time, and enhancing the overall efficiency of financial operations. 

MSP billing software saves time by integrating with PSA and accounting platforms. This eliminates manual data entry and ensures accurate, real-time client information, invoices, and payment data syncing.

Integrated billing software simplifies workflows by seamlessly connecting client service projects and deliverables into invoices, saving time and reducing manual billing tasks. It also gathers all data in one place, making it easier to create reports and giving a clear overview of finances and operations.

Similarly, MSP billing software eliminates these pains with automation, accuracy, and efficiency.

Unlike generic billing tools, MSP billing software is purpose-built to meet the unique needs of managed service providers (MSPs). A robust software automates repetitive tasks like sending invoices and following up on late payments, freeing your team to focus on strategic, high-impact activities such as service delivery and client acquisition. 

Real-time payment tracking ensures accurate billing, reduces disputes, and boosts client trust. 

In addition, automated payment reminders and multiple payment options help maintain a steady cash flow and prevent revenue delays.

Financial reporting is another critical advantage. With real-time insights into cash flow, outstanding payments, and billing trends, you can make smarter financial decisions and plan for sustainable growth. This financial visibility strengthens both stability and profitability.

For instance, an MSP that manages 50+ clients with diverse service agreements would use billing software to track payments, usage, and renewals smoothly. 

Automated billing sends timely invoices, resulting in steady cash flow, happier clients, and more vigorous financial health.

5 Key Features to Look for in Managed Services Billing Software

This section highlights essential billing software features you must prioritize: automation, financial reporting, and payment flexibility. 

Understanding these critical features lets you choose the right solution for efficient billing and sustainable growth. 

1. Automated Invoicing

Ardent Partners says automated invoices are processed 80% faster than manual invoices.

Automated invoicing enables you to generate, schedule, and send invoices automatically, reducing manual tasks and minimizing invoicing errors. 

Manual invoicing can be tedious and requires extensive data entry and reconciliation. Automation generates invoices based on pre-configured rules, service agreements, or usage data, allowing you to process billing quickly and consistently.

Streamlining invoicing boosts efficiency, enhances billing accuracy, and strengthens client trust, allowing them to focus on delivering exceptional service.

2. Recurring Billing

This helps automate the billing process for recurring charges, ensuring that clients are invoiced accurately and on time for subscription services, such as monthly maintenance plans, cloud hosting, or subscription software licenses.

One of the primary benefits of recurring billing is its ability to simplify monthly billing operations. 

For MSPs managing multiple clients and service tiers, manually tracking and invoicing recurring charges can be time-consuming and error-prone. 

Recurring billing automates this process, eliminating the need for repetitive data entry and ensuring that invoices are consistent and error-free.

3. Integrations

A survey of IT decision-makers found that a lack of integrated technology costs businesses an average of $500,000 annually.

Seamless integration with PSA and accounting tools is essential for your billing software.

This integration eliminates manual data entry by syncing real-time service details, invoices, and payments across all platforms. Additionally, integrations improve financial visibility and decision-making. 

Real-time synchronization lets you access up-to-date insights into revenue, outstanding invoices, and cash flow patterns from a single dashboard. 

This holistic view makes allocating resources better and planning financial activities easier.

4. Customizable Reporting

Reporting dashboards allow you to create tailored financial reports that provide insights into revenue, cash flow, and client payment trends. 

Unlike standard reports, a customized report will allow you to see key metrics like monthly recurring revenue (MRR) and outstanding invoices. With data, you can identify late payments, forecast cash flow, and improve financial planning. 

This proactive approach enhances decision-making, boosts operational efficiency, and strengthens financial stability for business growth.

5. Client Portals

According to LLCBuddy, a personalized client portal can help revenue rise by 10%-15%.

A robust client portal allows clients to easily access their billing history, outstanding balances, and payment methods, encouraging timely payments.

By providing transparency, it simplifies payments, reduces support inquiries, boosts trust,  and enhances the overall client experience.

This streamlined approach fosters trust, accelerates cash flow, and minimizes business administrative workload, leading to stronger financial health.

Top Managed Services Billing Software Options in 2025

In this section, we will review the leading MSP billing automation software. We focus on the key features, integration capabilities, and user feedback to aid MSPs in choosing the ideal billing software for their businesses. 

Each software review is structured to give a quick yet comprehensive overview of its utility for MSPs.

1. FlexPoint

FlexPoint is a billing, accounts receivable, and payment platform designed specifically for Managed Service Providers (MSPs) to simplify and automate their billing processes.

FlexPoint Features:

• Automated Reconciliation: Eliminates manual payment reconciliation between tools.
• AutoPay: Increases cash flow predictability through automatic payments.
• Branded Client Portals: These offer clients a white-label, user-friendly, secure payment portal to manage and pay invoices.
• Same-Day ACH: Unique to FlexPoint, Same-Day ACH enables MSPs to access funds on the same business day 5x faster than standard ACH.‍
• Dual-Sync Capabilities: bi-directional syncing available to automatically sync data across ConnectWise and QuickBooks Online.

FlexPoint Integrations:

• Accounting Systems: QuickBooks Online, QuickBooks Desktop, and Xero
• MSP-Specific PSAs: ConnectWise, Autotask, SuperOps,  and HaloPSA

Pros of using FlexPoint:

• FlexPoint’s client portal lets customers easily view invoices and make payments, improving their overall experience.
• The automation features for invoicing and payment processing reduce manual tasks, saving time and speeding up payment cycles.
• Multiple payment methods, including ACH (same-day ACH), credit card, and flexible financing.

Cons of Using FlexPoint:

• Limited direct integrations beyond PSA and accounting tools, but looking to expand shortly based on MSP/customer feedback.

FlexPoint Pricing Information:

• Pricing information is available on request. A scalable pricing model depends on MSP needs.
• Essentials Plan: Includes up to $50k in monthly processing and everything an MSP needs to get started
• Growth Plan: their most popular plan, with up to $100k per month in monthly processing and $50k of Same-Day ACH at no premium cost
• Plus Plan: Unlimited monthly processing with $100k of Same-Day ACH at no premium cost

FlexPoint Customer Review:

Here is a list of what customers are saying about FlexPoint:

• Pileus Technologies
• FortPoint IT
• Limetree Labs
• Pro IT
• Dega Systems
• Tomorrows Technology Today
• TAZ Networks
• IT Vortex
• Net-Tech
• Excellent Networks
• SkyCamp Technologies
• WJP Technology
• Circuit Saviors
• Compunet Technologies
• tekRescue
• Loud & Clear

2. ConnectBooster

ConnectBooster is a billing software designed to streamline accounts receivable for managed service providers.

ConnectBooster Features:

• Automated Dunning Notices: MSPs can configure and automate dunning notifications to send to customers who are behind on payments.
• Point-to-Point Encryption: The platform utilizes point-to-point encryption to protect customer credit card information throughout the payment cycle.

ConnectBooster Integrations:

• PSA: Autotask and ConnectWise.
• Accounting: Netsuite, Sage Intact, Microsoft Dynamics, and Xero. 

Pros of using ConnectBooster:

• It automates the entire invoice creation and delivery process.
• It offers detailed reports that provide insights into billing cycles, payment trends, and outstanding invoices.

Cons of using ConnectBooster:

• Does not offer a same-day ACH payment option.
• Its pricing can be a barrier for some businesses, especially smaller ones. 
• No financing options are available for your clients
• PCI compliance and email tracking come at an additional cost
• No automated deposit reconciliation capabilities

ConnectBooster Pricing Information: 

• $349/month

‍3. Alternative Payments 

Alternative Payments is a billing software for service-based businesses that simplifies invoicing, customer payments, and collections.

Alternative Payments Features:

• Flexible payment methods: Offers Buy Now, Pay Later (BNPL).
• Collections support: Reaches customers with overdue payments through various channels.
• Simple auto-pay features: reduce collection times.

Alternative Payments Integrations:

• Accounting Systems: NetSuite ERP, QuickBooks Online, QuickBooks Desktop, Xero, and others.
• MSP-Specific PSAs: ConnectWise, HaloPSA, SuperOps, and Autotask.

Pros of using Alternative Payments:

• It consolidates invoicing, customer payments, and reconciliation into a single platform.
• The platform also offers 60 days of onboarding and implementation support to ensure a smooth transition.

Cons of using Alternative Payments:

• It lacks some of the advanced reporting and analytics features other billing solutions offer.
• There are no automated deposit reconciliation capabilities available.
• Features such as client onboarding forms, scheduled payments, bulk payments, credit memos, and role-based permissions are unavailable.
• Some users have reported a lack of payment migration from the platform if you choose a different payment platform in the future.

Alternative Payments Pricing Information:

• $199 for transactions up to $50,000 monthly.
• $499 for transactions up to $100,000 monthly. ‍
• Custom: No transaction limit.

4. BenjiPays

BenjiPays offers integrated payment processing solutions to simplify financial transactions for small to medium-sized businesses.

BenjiPays Features:

• Integrated virtual terminal: It allows MSPs to process payments manually when needed, such as for phone or mail orders
• Integrated surcharging: This allows businesses to pass on credit card processing fees to their customers.

BenjiPays Integrations:

• Accounting: Xero and QuickBooks, and othersPSA: HaloPSA, ConnectWise,Autotask, and others

Pros of using BenjiPays:

• It integrates with popular accounting software like QuickBooks and Xero and various payment gateways.
• It will give you valuable insights into your financial activities.

Cons of using BenjiPays:

• It has limited customization and might not be suitable for businesses with very specific or complex needs.
• PSA integrations are available on select plans only.
• Features like automated deposit reconciliation, email tracking, onboarding forms, PSA & Accounting sync, and Same-Day ACH are not available.
• Does not currently offer financing options to MSP or clients.

BenjiPays Pricing Information:

• The Standard Plan: $129/month. Includes 100 approved transactions, with additional transactions at $0.80 each. 
• The Advanced Plan: $199/month. Includes the same transaction limit as the standard plan, with access to PSA integrations and other MSP-related features.
• The Elite Plan: $399/month. Includes 400 approved transactions, with additional transactions at $0.50 each.‍
• Enterprise Plan: Custom pricing – Tailored to meet the unique needs of larger businesses.

5. Zomentum 

Zomentum is a sales automation platform for MSPs with integrated payment processing capabilities. It allows businesses to accept payments directly within the platform.

Zomentum Features:

• You can quickly sign contracts electronically on the platform.
• Seamless payment process from quotes to e-signatures and final billing.

Zomentum Integrations:

• PSA: Syncro, RepairShopr, HaloPSA, and BSM by Kaseya
• Accounting: QuickBooks Online and Xero.

Pros of using Zomentum:

• It has e-signature functionality, allowing clients to sign documents electronically
• It allows for payment collection directly from the quote, automating invoicing and payment reminders

Cons of using Zomentum:

• Some users find the reporting feature in the Proposal & Quote Builder too basic and ineffective.
• The editing tool is too slow, and there is no undo.

Zomentum Pricing Information:

• Free access for 10 transactions a month
• $99 set-up fee

6. WisePay

WisePay is an integrated payment platform for Technology Service Providers (TSPs). It enables streamlined invoicing and secure transactions.

WisePay Features:

• Enhanced Security: Protection against cyber threats and unauthorized access.
• Comprehensive Reporting: Generates reports covering all aspects of financial transactions.
• Streamlined Reconciliation: Matches incoming payments with corresponding invoices or orders.

WisePay Integrations:

• PSA: ConnectWise and Autotask PSA.
• Accounting: Xero, Intuit QuickBooks, and others.

Pros of using WisePay:

• Customers can pay ad hoc invoices on demand via email links.
• Offers various payment methods, including credit cards, ACH, and direct debit.

Cons of using WisePay:

• According to current and past clients, AutoPay has very limited functionalities.
• It does not offer historical data within client payment portals, nor offer financing options for your clients.
• The onboarding process has been described as complex and multi-step. Its merchant account setup involves a Lengthy PDF application with a slow underwriting process

WisePay Pricing Information:

• Not publicly available. Custom pricing based on needs and requirements.

Conclusion: Choosing the Right Billing Software for Your MSP

In this article, we analyzed some of the best MSP billing software of 2025 for streamlining invoicing and automating payment tracking to enhance cash flow.

We also reviewed top solutions, including FlexPoint, ConnectBooster, Alternative Payments, BenjiPays, Zomentum, and WisePay, which offer unique features, pricing, and integrations to meet MSP-specific billing needs.

Selecting the right billing software for your MSP depends on your business model, service offerings, and client needs. 

The right solution can streamline operations, automate manual processes, and provide visibility into revenue streams. 

To make the best choice, you should evaluate their specific needs and focus on software features that align with operational goals and client demands. 

FlexPoint is a leader in this space with centralized management, customizable billing rules, and automation. 

By leveraging FlexPoint’s advanced capabilities, you can unlock new efficiency, accuracy, and client satisfaction levels.

Ready to transform your MSP’s billing operations? 

FlexPoint’s advanced billing solutions can streamline processes, improve client satisfaction, and boost financial efficiency. 

Schedule a demo today to see how FlexPoint can elevate your billing strategy in 2025.

Additional FAQs: Top MSP Billing Software

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