10 Best Billing Software Systems

FreshBooks No. 1 Alternative


One of the biggest revolutions in the software industry was the appearance of cloud-hosted accounting software, which rather than replacing dysfunctional Excel charts, covered operations companies weren’t even aware could facilitate financial management. Competent systems nowadays integrate perfectly billing and invoicing, and range from modest single-entry products to sophisticated bookkeepers to meet the needs of different businesses.

billing software systems

Billing and invoicing needs differ significantly from one company to the other, but what is very common in the corporate environment is to look for billing software that eliminates manual entries, and automates routine operations to cut time consumption. While it is almost impossible to discover a one-size-fits-all billing software system, there are ones that cater to most vertical industries, and incorporate configurable methods for payment collection to ensure usability on different markets. We’ve analyzed a large number of these products, and selected the leading top billing software solutions to help you make a more reliable choice for your business.

1. FreshBooks

FreshBooks is the highest rated system in our billing software category. Our experts firmly believe that FreshBooks can respond to the most important accounting needs of both small and large companies as it eases and tracks collection in a very reliable manner. It is also well known for its modern and beautiful interface, thanks to which even non-savvy users undertake and complete complex projects. To make this happen, FreshBooks offers a fully-featured invoice-to-payment suite where you can set due dates, charge late fees, brand invoices, send overdue reminders, and track billing.

This award is given to the best product in our Accounting Software category. It highlights its superior quality and underlines the fact that it's a leader on the market.
FreshBooks won our Best Accouting Software Award for 2018

On top of that, FreshBooks saves all of your billing history, reports on profits and losses, and handles taxation issues. If you want to try out this solution first there is a great free trial plan available (with no credit card required). You can easily sign up for FreshBooks free trial here.



  • United financial control. With FreshBooks, you can manage invoices and collect payments all in the same platform
  • Simple and intuitive interface. FreshBooks has a modern and easy-to-navigate interface for natural collaboration, and automates task prioritization.
  • Full invoice-to-payment suite. With FreshBooks, you can set invoice due dates, track billing and charge late payments, and collect finances making sure all taxation issues are taken into account.
  • Tracking expenses. In FreshBooks, you can log expenses with a single click, track those on daily basis, and use them for reimbursement deals.
  • Powerful reporting. FreshBooks processes data automatically, generates expense reports and balance sheets, and summarizes taxes.
  • Convenient pricing. FreshBooks’ monthly payments depend exclusively on the number of active clients in the system.
  • Integrations with a large number of third-party apps and lading credit card providers.
  • Fully functional mobile apps. FreshBooks helps take finances out of the office, namely to access records and do accounting on Android and iOS devices.


  • No invoice tags. Unfortunately, FreshBooks doesn’t offer invoice tags that could help customers find the invoice they’re looking for.
  • Doesn’t record non-billable expenses. For the moment, non-billable expenses should be entered in the system manually.
  • There is no Free Plan for small teams and sole accountants.

2. Intacct

Intacct is foremost an ERP system which can also be used for billing and invoicing in small and medium business environments. It offers a well-organized and reliable financial management suite, and helps even non-accountant users manage multi-currency transactions and make accurate productivity projections. Reporting is very flexible, but the system also offers ready-to-use templates for standard balance sheets and payment monitoring. At the same time, Intacct can respond to users’ accounts payable and accounts receivable operations, track fixed assets, and manage their inventory.



  • Depreciation tracking. Intacct is probably the only system on this list that enables users to track depreciation rates.
  • Simple and clean interface. With a bit of digitized accounting experience, the user will have no trouble learning to navigate Intacct. The Dashboard and all of its options are fully customizable.
  • Core accounting capabilities. Designed as an ERP system, Intacct is packed with functions that lower revenue risks, and help users regain control over their costs and margins.
  • Creative multicurrency management & compliance. Intacct  lessens the burden of computing for currency differences from small-scale transactions, such as, vendor management to highly complex international transactions.
  • Built-in report templates. Intacct helps even non-accountant users understand critical metrics, and calculate KPIs, returns, and commissions, and to make transactions more transparent.


  • Transferring corporate data to the system requires professional help.
  • Training is limited for basic users.
  • No fixed pricing scheme – you have to contact the company to get a quote.

3. Zoho Books

Zoho Books is one of the most prominent members of Zoho’s productivity family, designed to facilitate financial management in small and medium business environment. The cash flow control it provides helps companies grow and develop, as they can automate invoicing and collect payments all from a single platform. What makes the system unique are automated bank feeds and live collaboration with clients, while you can also use it to manage your inventory, track time and manage projects, and facilitate reconciliations using Stripe.



  • Automated bank feeds. Zoho Books imports all bank and credit card transactions to save time and align your operations to bank rules.
  • Online collaboration with customers & contact management. Zoho Books is one of the rare systems that lets you involve customers, namely letting them access their estimates, track bills, and make online payments through the same portal.
  • Facilitated reconciliation. Zoho Books integrates with Stripe to reconcile transactions, and to give you the full picture of how money is moving in and out of your accounts.
  • Stock and inventory management. With Zoho Books, you can create and track purchase orders and run inventory reports in less than no time.
  • Retainer invoices. Zoho Books covers companies and sole accountants collecting prepayments and retainers for the time they spent working. For the purpose, the system records offline payments, and associates them to the final invoices.
  • RESTful API for unlimited integrations. Thanks to its rest-based API, Zoho Books can work in every software infrastructure.


  • Custom reporting is slightly more limited than compared to the one of FreshBooks.
  • Won’t work for large enterprises.
  • No Free Plan for sole accountants

4. QuickBooks

QuickBooks is another top billing software, often praised for delivering enterprise-acquired value to mid-market and enterprise-grade users. The platform embeds all core invoicing functionality, and brings all bills and overdue items under the same roof for easier tracking and payment collection. Reporting is fully customizable and able to cover all transactions, and information is fully secured according to the highest protection standards.



  • A handy Bill Tracker and one-click payment. QuickBooks assembles all transactions and bills in the same system, where your customer can track their status and complete payment by clicking on a single button.
  • Collects and analyzes large volumes of data. Enterprises like to think of QuickBooks as their BI system, as the amount of data and the payroll they run and process don’t compromise its functionality.
  • Automated and customizable reporting. With QuickBooks, you can customize all your reports and schedule them in a calendar.
  • Inventory and shipping management. QuickBooks is particularly rich with packaging options, and will cover even those you were missing with your standard accounting system.
  • Flexible deployment. You can choose whether you want to deploy QuickBooks in cloud or on premise.


  • May appear too complex to novice users. If you’re new to the whole digitized accounting thing, QucikBooks’ multiple menus may take a while to learn.
  • Without accounting experience, customization may require professional help.
  • Doesn’t offer a Free Plan for sole accountants.

5. Xero

Xero is another top performer in our Billing & Invoicing category, often targeted as market’s best financial collaboration system. The business value of this product consists in transforming standardized and complex financial concepts into operations understandable even for non accountants, and the multiple connections to third-party software that helps you extend its functionality. You can set it up in less than no time, and use its premade templates to simplify transactions and make them more business-specific. Xero is also handy for managing robust inventory (adjust taxes for more than 20 states), and pulls off awesome reports including Cash Flow Records and Income Statements.



  • Standardized accounting logic. As robust and powerful as it is, Xero still allows accountants to work in a familiar environment and customize their operations.
  • Small-biz friendly Expert Setup. Small teams with modest accounting needs looking to move money quickly can consult Xero for express setup options.
  • A single dashboard to compare all finances. Xero’s functionality is bundled in seven tabs where you can create records for all payroll needs, enter all your information, find and alter checks, bank accounts, and expense claims.
  • Transactions made simpler. The system offers ready-to-use templates and transaction forms, and minimizes the risk of financial fraud with two-factor authentication.
  • Transformed inventory management. Xero also processes and runs payrolls, and automatically adjusts taxes for more than 20 states. It also offers a Stock Management Powerhouse where you can create tax status and purchase records, and add them to your transactions.


  • Bank account data cannot be synced for reconciliation. Instead, you have to upload it yourself.
  • Not all expenses can be displayed in a different currency.
  • No Free Plan for sole accountants.

6. Tipalti

Tipalti is a secure and fully-compliant financial system that helps users eliminate the administrative overload and automate payments in more than 190 countries. It also ensures that you will meet all taxation and regulatory requirements, and improve customers’ experience regardless of the complexity of your operations. Tipalti is functional in Network Economy companies with high volume and high complexity global pay operations, but also ISPs, affiliate networks, advertising network, online marketplaces, and many more.

Tipalti F


  • Automated payment. Tipalti automates over 50% of all manual, global, and pay out operations in more than 190 countries.
  • Remittance Validation Engine. In Tipalti, all operations are conducted on a brandable Supplier Management portal, where all inserted taxation info is then validated by a homegrown Remittance Validation Engine that monitors 26,000 national and international standards.
  • 120 currencies and 6 payment methods. With Tipalti, the user can choose between 120 currencies and 6 payment methods (Paypal, Wire, Prepaid Debit Card, US ACH, Global ACH, or Local bank transfer).
  • Top notch reporting. Tipalti’s reporting is distinguished by a variety of out-of-the-box details that catch the attention of modern business owners, including taxation rules, disparate payment method strategies, or regional considerations.
  • Payment fraud detection. With payment processing regulatory compliance, reconciliation, and 1042-S tax reports, Tipalti helps prevent and detect fraud.


  • Single payment plan. Tipalti’s pricing is not exactly flexible, as there is a single plan instead of annual subscriptions and one-time payment options.
  • Limited customization.
  • No free plan for startup businesses and sole accountants.

7. Harvest

Harvest is a reputed business management app designed to facilitate billing and invoicing. It helps design and distribute professional invoices, but also remain in control of payment operations with a handy reporting suite. It tracks time and expenses, and automates notifications to cultivate productivity and accelerate growth. It is fully compatible with all mobile devices, and integrates with a wide range of third-party applications.

Harvest F


  • Simple and intuitive interface. With Harvest, most payment operations are conducted with a single click.
  • Automated report notifications. With Harvest, employees get their weekly timesheets where they insert information on their activities.
  • Powerful time tracking. Harvest is known for its advanced time tracking capacity, and integrates with a large number of third-party apps to help monitor operational progress.
  • Multiple add-ons. In essence, Harvest’s invoicing capabilities are very basic, but there are a number free add-ons you can install to extend its functionality.
  • Flexible payment scheme. Harvest’s pricing depends on the number of users, and there are 3 affordable plans to choose from (Solo, Basic, and Business).


  • 3 Access Levels, where permissions depend exclusively on the administrator. Harvest’s strict hierarchy allows users to participate only in projects ascribed to them, which happens to limit creative teams.
  • Insufficient exporting functions. The only exporting options Harvest provides to its users is to export all data, instead of a particular portion.
  • You can’t report per project.

8. PaySimple

Just as it can be concluded by the name, PaySimple automates transactions, and gives businesses the tools they need to bill customers and monitor their details, receive payments, and set up recurrent payment systems. As intuitive and user-friendly as it is, PaySimple work well for companies but also end users, who simply love how fast and secure they can complete their payments. At the same time, PaySimple can be used for booking and effective time management.

Paysimple F


  • Monitoring customers with pertinent details. With PaySimple, you get to monitor details such as saved credit card and banking information which are also re-saved for further usage.
  • A secure and powerful payment collection platform. With PaySimple, users can accept credit cards, debit cards, and ACH e-checks, making it easy and convenient for their clients to choose their preferred mode of payment.
  • Great collection software. PaySimple can also be used as a convenient collection system and an online booking tool that showcases your services.
  • Handy Calendar application. PaySimple offers also a Calendar application where you can follow all appointments, and automate follow-ups and reminders.
  • Customer management. PaySimple helps small companies by offering contact management, and eliminating the need to use additional CRM systems.


  • Making changes on payment details is not intuitive. Most of the time, PaySimple will expect you to entirely delete old credit card info before you’ve changed it.
  • No multicurrency or multilanguage service.
  • No Free or Basic plan for small businesses.

9. Bill4Time

Bill4Time is a time tracking and invoicing platform that is designed for the needs of accountants and law practitioners and can also be used by other types of professional services providers. It helps them to boost their productivity and deliver high-quality services to their customers. This full-featured management suite can be used to handle reporting, accounting, projects, and clients. Apart from timekeeping and billing, you can utilize the software to generate and deliver invoices to clients, organize documents, set schedules, perform accounting tasks and more.


  • Tracks time effectively. Bill4Time simplifies the allocation of time worked to a specific client or project and the import of hours worked from Excel spreadsheet.
  • Bill clients easily. The software supports hourly billing, a flat rate, and contingencies.
  • Add branding elements. You can add your text and logos to your invoices to provide a customized look to the documents.
  • Improves transparency. You can give permission to your clients to review their billing rates and invoices, and provide feedback.
  • Payment flexibility. The platform integrates seamlessly with a range of widely used payment gateways and channels including PayPal, Quickbooks and other credit card processors.
  • Project management feature. This feature enables you to plan, organize, track, and, run your business in a better manner. It helps you to streamline workflows, increase productivity, and enhance efficiencies.


  • More features could be added. The vendor could add CRM and resource management tools to increase the overall effectiveness of the software.

10. Moon Invoice

Moon Invoice is an easy-to-use solution for handling your invoicing needs on an intuitive interface. It touts a high degree of customizability as well for its invoices, allowing you to create and send personalized invoice templates with ease. Featuring applications not only for Windows and macOS but also for Android and iOS, Moon Invoice is an ultra-ambulatory solution that enables users to stay on top of their businesses operations anywhere and anytime. It also comes equipped with time tracking, direct conversion of estimates into invoices, PDF-embedded payment options, tasks management, expense tracker, and other tools to ensure a steady cash flow for your business.



  • Invoicing on-the-go. With its native apps for both Android and iOS, you can create, manage, and track invoices as needed.
  • Convenient payment options for clients. You can provide customers with great convenience for settling their balances through PDF-embedded payment options. Basically, your clients can find the right links to online payment gateways forpaying their balances.
  • Time Tracking. Correctly bill clients with its time tracking capability.
  • Convert estimates. With Moon Invoice, you no longer have to worry about having instances of double data entry, as the platform can convert your estimates into invoices.


  • You are unable to receive confirmation that customers have received and viewed your invoice.
Category: B2B News

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