FlexPoint has made my job easier because I can depend on invoices to go out without oversight, and I'm notified about absolutely every payment and message. It's reduced my accounts payable/receivable workload by 75%.

Juli Brinkley

Loud & Clear

FlexPoint's Working Capital Solutions have been crucial in helping Loud & Clear expand its services to enterprise-level clients. The boost in our number of clients & annual revenue has been staggering.

Patrick Kemp


FlexPoint has made my job easier because I can depend on invoices to go out without oversight, and I'm notified about absolutely every payment and message. It's reduced my accounts payable/receivable workload by 75%.

Juli Brinkley

Loud & Clear

FlexPoint's Working Capital Solutions have been crucial in helping Loud & Clear expand its services to enterprise-level clients. The boost in our number of clients & annual revenue has been staggering.

Patrick Kemp

5 Leading MSP Payment Reconciliation Software Tools to Streamline Your Billing

Discover the top five MSP payment reconciliation software tools to streamline your billing process. This guide highlights key features, benefits, and integration options, helping you choose the best solution to reduce errors and improve financial accuracy for your MSP.

Victor Lopez
CEO of FlexPoint



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For MSPs, recurring payment issues can drain resources and negatively affect client satisfaction. A solid payment reconciliation software can transform this process, minimizing errors and significantly improving operational efficiency. With automated systems, you can track and analyze in real-time, ensuring that every transaction is accounted for and every discrepancy is promptly addressed.

This post will explore five leading MSP payment reconciliation software tools that can streamline your billing process. Adopting the right software allows you to focus on growing your business and providing exceptional service to your clients.

What is MSP Payment Reconciliation Software?

Payment reconciliation is comparing and verifying financial records to ensure that the amounts received match those invoiced or recorded in the accounting system. The process is crucial for maintaining accurate financial records, preventing discrepancies, and ensuring all transactions are accounted for correctly. 

Accurate reconciliation helps businesses avoid potential financial losses, improve cash flow management, and maintain trust with clients and stakeholders.

An MSP payment reconciliation software automates matching invoices and payments and bank deposits –  significantly reducing human error and saving time for more critical tasks, such as cash flow management, operational improvements, compliance and auditing, and financial analysis.

Unlike generic payment software, MSP payment reconciliation software is specifically designed to meet the unique needs of MSPs, considering factors such as recurring revenue, multiple client management, complex integration requirements, and stringent security requirements.

MSP Payment Reconciliation Software is a specialized tool designed to streamline and centralize billing and financial management for Managed Service Providers (MSPs). This software integrates seamlessly with popular MSP tools like ConnectWise and Kaseya and accounting software like QuickBooks Online, Quickbooks Desktop, and Xero, ensuring accurate and real-time financial data records. Automating repetitive tasks and reducing errors allows MSPs to save time on administrative work and focus on delivering quality services. 

Benefits of MSP Payment Reconciliation Software

MSPs benefit from using payment reconciliation software to manage high-volume billing and invoicing efficiently, reducing errors and improving financial tracking. 

There's a 36% chance your MSP's finance team is wasting 9 hours on reconciliation every month, effectively losing at least one full day of work. You need payment reconciliation software to streamline financial management and stop this inefficiency. 

Let’s look at the other benefits of using robust payment reconciliation software.

  • Reduced Operational Costs: Automated payment reconciliation ensures timely and accurate financial records, enhancing operational efficiency and cost savings. For instance, IT Vortex, a Paramus, NJ-based MSP, saves $15,000 monthly on invoicing through automation. Automated systems handle recurring billing, generate invoices, and reconcile payments with minimal human oversight, saving about 60 hours per year in manual invoicing and labor costs.
  • Enhanced Billing & Invoicing Accuracy: Payment reconciliation software minimizes human error and prevents fraud in billing and invoicing systems. According to the ACFE (The Association of Credit Fraud Examiners, businesses typically lose about 5% of annual revenue to fraud due to financial irregularities. A robust reconciliation software can significantly reduce this risk. For example, payment reconciliation software employs automated matching of invoices to payments to bank deposits, flagging discrepancies for review and providing audit trails for all transactions. This allows MSPs to quickly identify and resolve issues, avoiding fraud and boosting efficiency.
  • Improved Cash Flow Management: For MSPs with multiple clients, payment reconciliation software ensures you keep track of hard-earned revenue. Atradius reports that over 50% of late payments are never collected. Reconciliation software improves cash flow management by automating the tracking of incoming and outgoing payments, sending reminders for overdue invoices, and providing real-time financial analysis. This allows MSPs to quickly identify and address revenue leakages, ensuring a steady and predictable cash flow.
  • Compliance & Security: MSPs are crucial in protecting SMBs from cyber threats, yet they often overlook payment security. Accepting checks and credit card payments over the phone are major security risks, exposing sensitive information to fraud and theft. It puts MSPs at a risk of non-compliance with payment standards/regulations such as PCI-DSS. A robust MSP payment software mitigates these risks by encrypting financial data, implementing secure payment methods, and ensuring regulatory compliance. These essential security features protect MSPs and their clients from cyber threats and safeguard sensitive financial information.
  • Scalability: As MSPs grow and handle multiple clients, they need a reliable payment reconciliation system to minimize activities or tasks that can hinder business growth. Nearly 65% of businesses believe payment reconciliation is the most labor-intensive process, highlighting the need for efficient solutions.
  • Client Satisfaction: Prioritizing payment reconciliation is essential for reducing client churn and ensuring satisfaction. Reconciliation software reduces payment friction and improves customer satisfaction by promptly tracking and analyzing payment and billing issues. According to Khoros, 83% of customers are loyal to companies that listen and resolve their problems. The last thing you want is recurring payment issues with clients — it's draining for your MSP and could adversely affect customer satisfaction.

How to Choose the Right MSP Payment Reconciliation Software

When selecting MSP payment software, consider factors that align with your business needs, workflow, and long-term goals; here's a checklist to guide you:

  • Essential Features: Ensure the software offers core functionalities such as automated reconciliation, recurring billing, customized invoicing, and the ability to manage multiple service packages. It must integrate seamlessly with your existing Professional Services Automation (PSA) tools (such as Connectwise and Autotask). Automated reconciliation, for instance, saves hours of manual work and reduces errors, enhancing day-to-day operational efficiency.
  • User Experience: Choose software with a user-friendly interface to facilitate easy navigation and quick adoption by your staff and, most importantly, for your MSP clients. A well-designed interface minimizes training time and maximizes productivity, allowing your team to focus on higher-value tasks.
  • Pricing and Purchasing Terms: The best pricing structure for MSPs is typically a subscription-based model, as it offers predictable costs and scalability. Transaction fees can be a secondary option but may fluctuate based on volume. Evaluate options for flexible contracts to find a solution that aligns with your financial planning.
  • Compliance and Security: Confirm that the software meets relevant financial regulations and data security standards. Robust security measures, such as two-factor authentication and encrypted data storage, are critical for protecting sensitive financial data and maintaining compliance with standards like PCI DSS.
  • Integrations: Ensure seamless integration with your existing accounting software (e.g., QuickBooks Online, Quickbooks Desktop, Xero) and RMM tools (e.g., ConnectWise, Autotask). This two-way integration significantly enhances operational efficiency by streamlining workflows and eliminating manual data entry.
  • Client Onboarding and Experience: Opt for features that enhance the client experience, such as self-service portals and automated payment reminders. A smooth onboarding process ensures clients can easily access invoices and make payments, reducing friction and improving satisfaction.
  • Customer Support: Reliable and responsive customer support is essential for addressing any issues or queries arising during the software's implementation and ongoing use. Quick resolution of problems minimizes downtime and maintains business continuity.
  • Vendor Reputation: Research the vendor's reputation and track record in the industry. Read online reviews, seek references from other MSPs, and evaluate the vendor's stability and support services. This provides valuable insights into the user experience and the software's long-term viability.
  • Scalability and Future-Proofing: Consider the software's ability to scale with your business growth. Evaluate its roadmap for future updates and enhancements to ensure it remains relevant and continues to meet your evolving needs. Scalable solutions prevent the need for frequent software changes, saving time and resources in the long run.

Review of Top 5 MSP Payment Reconciliation Software

Managing payment reconciliation is vital for Managed Service Providers (MSPs) to maintain accurate financial records and streamline operations. The right software can automate the reconciliation process, reduce errors, and save valuable time. 

We will review the top five MSP payment reconciliation software solutions, highlighting their key features, integration, pricing, customer review, pros, and cons.


FlexPoint Home Page

FlexPoint offers a robust payment reconciliation solution designed to streamline and automate your financial processes, making it easier to manage your cash flow and ensure accurate payments. 

Flexpoint Features

  • AutoPay: Increase cash flow predictability by creating custom rules for automatic payments. Apply these rules to all clients or tailor them to specific ones.
  • Automated Reconciliation: Eliminate manual payment reconciliation between your tools. Easily view payment deposit details and ensure accuracy without manual effort.
  • Branded Client Portals: Offer your MSPS clients a fully branded, user-friendly, and secure payment portal to manage their invoices and payments, thus enhancing brand trust and optimal client experience.
  • Real-Time Tracking: Keep track of every invoice, payment, and deposit. Always know where your money is and when you'll get paid, ensuring timely and accurate financial management.

Flexpoint Integrations: 

  • Accounting System: Quickbook Online, Quickbook Desktop. And Xero.
  • MSP-Specific PSA: Connectwise, Autotask, Halopsa.

Pros of Using Flexpoint

  • FlexPoint reduces 5 hours of manual work per month to just 15 minutes through automated invoicing and reconciliation processes.h
  • FlexPoint provides a client portal for easy viewing and payment of invoices.
  • FlexPoint offers flexible month-to-month contracts plan without long-term commitments.
  • FlexPoint offers end-to-end automation, reducing the time required for accounting and reconciliation tasks.

Cons of Using Flexpoint

  • Limited integration options, but actively expanding.

Flexpoint Pricing Information

  • Custom pricing tailored to your MSP's financial needs is available. 
  • Contact the FlexPoint team for a demo and detailed pricing information.

Flexpoint Customer Reviews

  • Customers like Flexpoint because it streamlines their financial processes with features like a client portal for easy payments and automated invoicing that saves. 

Here is what some customers have to say about Flexpoint.


Stripe Home Page

Stripe, although primarily known for handling online payments, also offers capabilities that support reconciliation processes, making it a valuable tool for Managed Service Providers (MSPs). Here's what you need to know about using Stripe for payment processing and reconciliation:

Stripe Features:

  • Payment Processing: Its robust infrastructure supports multiple payment methods, currencies, and countries, ensuring that MSPs can manage payments globally.
  • Developer-Friendly APIs: MSPs can integrate Stripe seamlessly into their existing systems, creating tailored payment solutions that fit their needs. 
  • Reconciliation Features: While not a dedicated reconciliation software, Stripe provides features that aid the reconciliation process. It offers detailed transaction reports, real-time payment tracking, and automated invoice generation. 
  • Real-Time Reporting: Transparency helps MSPs monitor their cash flow, identify discrepancies early, and maintain an accurate financial health overview.

Stripe Integrations: 

  • Accounting System: FreshBooks, Wave, QuickBooks Online Advanced, Patriot Accounting, and SaasAnt Transactions.
  • MSP-Specific PSA: Autotask, Atera, Halo PSA, Syncro, and Kaseya BMS.

Pros of Using Stripe

  • "Easy to deploy and has various integrations available" - Capterra
  • "It's also very easy to manage and keeps tabs on everything happening on your account even on your phone" - Capterra
  • "Easy to implement to the system, and it is the main payment gateway of our business." -G2
  • "The setup process was simple, and the fees are very reasonable." - GetApp

Cons of Using Stripe

  • Reconciling payments to orders is challenging with Stripe due to their use of non-specific hash codes, lumped payments, and multiple daily transfers
  • "Several client transactions in one payment - reconciliations are extremely difficult"- Capterra
  • "Some cards are not acceptable, which creates some time issues for clients." - G2
  • “It takes a few days for payments to be deposited into the bank account." -GetApp

Stripe Pricing Information

  • There are two main pricing structures for Stripe:some text
    • Standard Plan: Ideal for online transactions, stripe charges 2.9% + 30 cents per successful domestic credit card transaction.
  • Additional Services: For swiped (in-person) payments and general payment processing, the rate is slightly lower at 2.5% + 20 cents per successful card charge.

Stripe Customer Reviews

  • Customers like Stripe for its ease of use, clear APIs, smooth integration, and simple setup process. However, they say it takes days to receive a deposit.some text
    • Software Advice: 4.6
    • G2: 4.3
    • GetApp: 4.6


 PayPal Home Page

PayPal is a renowned online payment platform that, although not designed as a reconciliation tool, has features that help MSPs in payment processing and reconciliation. Here's a brief overview of PayPal's capabilities and features:

Paypal Features

  • Payment Gateway: PayPal is a reliable payment gateway that facilitates online transactions between MSPs and their clients. 
  • MSPs and Client Protection: PayPal offers robust security features, including buyer and seller protection. These protections help MSPs maintain client trust and ensure safe financial transactions.
  • Reconciliation: While not a dedicated reconciliation tool, PayPal provides detailed transaction histories and comprehensive reporting capabilities. MSPs can use these features to track payments, match transactions with invoices, and maintain accurate financial records.

PayPal Integrations: 

  • Accounting System: Zoho Books, QuickBooks Online, Xero, Wave, and SaasAnt Transactions
  • MSP-Specific PSA: Syncro, Computicate PSA, and HaloPSA.

Pros of Using PayPal

  • "The software was easy to implement and manage." - Capterra
  • "The company was amazing at customer service." - Trustpilot
  • "The speedy process of payments is definitely what I like most." - GetApp
  • "PayPal is a secure online platform to receive and send payment digitally." - G2

Cons of Using PayPal

  • PayPal provides no reasonable means to reconcile transactions to your account register.
  • PayPal seems to go out of its way to make reconciliation impossible.
  • I plan to use the card a lot less; the time involved with reconciling the accounts is not worth the cashback.
  • "They limited my account for 180 days, and I had a lot of cash to withdraw." - G2

PayPal Pricing Information

  • PayPal charges a standard rate of 2.9% plus a fixed fee for domestic transactions. However, international payment attracts additional fees based on the currency and standard cost.

PayPal Customer Reviews

  • Customers appreciate PayPal's ease of use, fast transaction speeds, and secure online payment system, but some find the fees for international payments high, and the layout could be improved.some text
    • Software Advice: 4.7
    • GetApp: 4.7
    • G2:4.4


Quickbooks Home Page

Quickbooks is a comprehensive accounting software that provides a range of features tailored to meet the needs of Managed Service Providers (MSPs). Here's what you should know about using Quickbook for payment reconciliation: 

Quickbook Features:

  • Accounting: QuickBooks offers extensive accounting functionalities, including invoicing, expense tracking, and financial reporting. MSPs can manage their financial operations efficiently, ensuring that all financial transactions are accurately recorded and monitored.
  • Reconciliation: QuickBooks simplifies bank reconciliation by allowing users to match bank transactions with their internal records. This feature helps MSPs track transactions, identify discrepancies, and ensure their financial records are accurate and up-to-date. 

Quickbook Integrations: 

  • MSP-Specific PSA: Accelo, HaloPSA, Syncro, and Computicate PSA.
  • Payment Integration: Veem, PayPal, Google Pay, and Stripe

Pros of Using Quickbook

  • "Quickbooks is super user friendly." - Capterra
  • "Banking feeds are good to use for the reconciliation." - G2
  • "The payment processor is easy, well-known by customers so trustworthy." - Software Advice
  • "Fields to fill and perfectly links the data from one end like ap and AR to the bank reconciliation." - GetApp

Cons of Using Quickbook

  • "Reconciliation of the books can be confusing to do alone." - Capterra
  • "It confused us to use the right categories at first." - G2
  • "It is next to impossible to change something if the bank reconciliation is done" - Software Advice
  • "Customer support needs to be more easily reachable" - GetApp 

Quickbook Pricing Information

  • QuickBooks offers tiered monthly subscription plans with varying features.some text
    • Simple Start: $15/month (discounted to $7.50 for the first three months)
    • Essentials: $30/month (discounted to $15 for the first three months)
    • Plus: $45/month (discounted to $22.50 for the first three months)
    • Enterprise: Custom pricing for advanced features like inventory management.

Payment Processing Fees:

  • In addition to the monthly subscription, QuickBooks charges a separate fee for processing payments. These fees vary depending on the payment method:some text
    • ACH Bank Transfers: 1%
    • Credit/Debit Cards: 2.99% (Visa, Mastercard, Discover, American Express)
    • Digital Wallets: 2.99% (Apple Pay, PayPal, Venmo)
    • Card Reader Transactions: 2.5% (Visa, Mastercard, Discover, American Express, Apple Pay, Google Pay, Samsung Pay)
    • Manually Entered Card Information: 3.5% (highest fee)

Additional Payment Fees:

  • Introductory discounts: You get an introductory discount for the first three months only.

Quickbook Customer Reviews

  • Customers love QuickBooks for its ease of use and centralized features, allowing them to manage finances, payroll, and invoicing in one place. But, some complain about the customer service.some text
    • GetApp: 4.3
    • Capterra: 4.3
    • G2: 4 


Xero Home Page

Xero is an accounting software with robust reconciliation functionality, making it an excellent choice for Managed Service Providers (MSPs). Here's what you should know about using Xero for payment reconciliation:

Xero Features:

  • Accounting: Xero offers invoicing, expense tracking, and financial reporting.
  • Bank Reconciliation: Allows matching payments with bank statements.
  • Split Transactions: If an amount is underpaid or part of a payment needs separate accounting, Xero lets you split transactions during reconciliation.
  • Find & Match: Xero allows you to match relevant transactions to bank statement lines. This feature helps ensure accurate reconciliation

Xero Integrations: 

  • MSP-Specific PSA: Naverisk, Syncro, Atera, and Autotask PSA
  • Payment Integration: PayPal, Stripe, and Square Point of Sale

Pros and Cons of Using Xero

  • "Xero seamlessly connected and kept my balances up to date." - Capterra
  • "Automating the process of bank reconciliation is amazing time saver, it connects to banks and credit cards." - GetApp
  • "I love its reconcilitation features" - G2
  • "It is a convenient tool for bank reconciliation." - Software Advice

Cons of Using Xero

  • "Unfortunately, the reconciliation process in XERO is a no-go for me." - Capterra
  • "Bank reconciliation has been automated but the process got glitches causing bank feeds  to stop" - GetApp
  • "We cannot import CSV for booking prepayments in Xero" - G2
  • "Reports are impossible to configure and source the data I need." - Software Advice

Xero Pricing Information

  • Early: $15
  • Growing: $42
  • Established: $78

Xero Customer Reviews

  • Customers like Xero for its ease of use, cloud-based accessibility, and integrations with services like Stripe. However, recent price increases and occasional forced updates must be more manageable.some text
    • Software Advice: 4.5
    • Trust Pilot: 4.2 
    • GetApp: 4.4
SoftwareAutomated ReconciliationRecurring BillingCustomized InvoicingIntegrationsSecurity FeaturesClient OnboardingReporting and Analytics
FlexPointYesYesYesConnectwise, Autotask, Halo, Quickbooks, XeroPCI DSSYesYes
StripeNoNoNoAtera, Syncro, Autotask, Halo PSA, Zoho Books, TaxDome, Kaseya BMSPCI DSS, GDPR, SOC 2NoYes
PayPalNoNoNoCloudBlue PSA, computicate PSA, FreshBooksPCI DSS, GDPR, SOC 2NoYes
QuickBooksNoYesYesHaloPSA, computicate PSA, Accelo, SyncroPCI DSS, GDPR, SOC 2NoYes
XeroNoYesYesAtera, Naverisk, Syncro, Autotask PSAPCI DSS, GDPR, SOC 2NoYes
Summary Table: MSP Payment Reconciliation Software

Conclusion: Streamline MSP Billing with the Right Payment Reconciliation Software

In this article, we’ve highlighted the challenges MSPs face with manual payment reconciliation, such as inefficiencies, errors, and resource constraints. To address these issues, we reviewed top MSP payment reconciliation software that streamlines billing, enhances accuracy, and provides real-time financial insights.

Choosing the right software is crucial for optimizing payment processes and overall performance. 

FlexPoint stands out with its comprehensive tools for MSPs for billing, invoicing, and especially reconciliation. For example, FlexPoint significantly transformed Excellent Networks' payment reconciliation process by automating invoicing and payment collection. By integrating FlexPoint, Mark saved several hours per month in billing time.

By leveraging FlexPoint's automated reconciliation capabilities, MSPs can significantly reduce manual labor, minimize errors, and ensure timely and accurate financial records. This enhances operational efficiency and improves cash flow management and customer satisfaction. 

Ready to transform your payment reconciliation processes? Explore FlexPoint's features by scheduling a demo today to see how it can revolutionize your MSP billing and reconciliation processes.

Frequently Asked Questions (FAQs): MSP Payment Reconciliation Software


Can MSP Payment Automation Software Improve Client Relationships?

Of course, by using MSP payment automation software, client relationships can be significantly improved with features like transparent billing, easy payment options, and a streamlined interface. These characteristics provide a client with an excellent understanding of billing processes that, in the end, can result in growth in client satisfaction and trust.

How Does MSP Payment Automation Software Integrate With MSP Management Tools?

The MSP payment automation application should be able to communicate with other applications, such as professional services automation (PSA). This allows MSPs to see the full picture of their client service delivery, including invoicing, billing, finances, etc. 

What Security Features Should I Look For in MSP Payment Reconciliation Software?

When selecting MSP payment reconciliation software, prioritize robust security features such as encrypted data storage to protect sensitive financial information, two-factor authentication (2FA) to enhance access control, and compliance with industry standards like PCI-DSS. Additionally, look for software that offers regular security updates and audits to ensure ongoing protection against emerging cyber threats.

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