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Best Accounting Software For Ecommerce: Manage Your Accounting With Ease!

Best Accounting Software For Ecommerce: Manage Your Accounting With Ease!

Accounting is non-negotiable if you want run a successful ecommerce business. It is easy to find yourself overwhelmed by the administrative tasks you need to handle. Worst of all, breaking accounting rules (intentionally or not) can be cost you a pretty penny, stressful, and sometimes even considered a crime.

In this article, we will look at some of the best accounting tools for ecommerce. Each app we will cover has at least one unique strength.

Key Features of Accounting for Ecommerce

There are many ecommerce accounting software programs: there are paid multifunctional software and free accounting software programs with a limited set of features. There are also online services that allow you to do ecommerce accounting through a browser.

Before choosing one or another program for accounting, it is necessary to analyze your company's work. Choose the software depending on your sales funnel, the documents you use and what tax system and reporting are used at your firm. The best accounting software can perform a huge number of functions. However, there is a certain set that is common to every accounting program, they include:

  • All aspects of dealing with primary documents;
  • Carrying out the necessary accounting calculations;
  • Analysis of current legislative articles;
  • Drawing up a register of all business operations;
  • Working on accounting forms;
  • Working with the assets and liabilities of the enterprise.

If you need to do accounting for a small or medium ecommerce business, the company can get by with a set of preinstalled functions, which will not change. If we are talking about a large enterprise with many subtleties in accounting, you should choose software that allows you to integrate additional options or applications.

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Accounting for Ecommerce: Necessary Aspects and Features to Consider While Choosing Accounting Software

1. Bank Feed

Bank feed is absolutely necessary for any ecommerce accounting program. With this feature, you will receive daily updates on your account and transactions in your ecommerce platform. No more manually uploading all transactions into the system - the software will do it for you. Besides, you will be able to get a daily overview of all your accounts, which helps reconciliation and takes most of the burden off you or your accountant.

bank feed in the Intuit QuickBooks ecommerce accounting platform

2. Online Invoicing

Online invoicing is one more ecommerce-specific feature of an accounting program. It allows you to send invoices by email (or other channels) and accept payments online. Depending on which software you choose, it may require you to use its own data processing features, or it may provide the ability to integrate with third-party software. Also, it can generate invoices on its own.

3. Recurring Invoices & Payment Reminders

Schedule the automatic generation and sending of invoices with recurring payments - for example, if you provide a subscription service. You can send invoices weekly, monthly, annually, or even daily - most importantly, remember to specify an end date for billing. You can also remind customers about an upcoming payment - or that a payment is overdue.

4. Bank Reconciliation

Smart reconciliation calculates potential matches that may appear between the accounts listed in the program and your bank transactions and accounts. This saves time that is often spent manually sifting through information. You can manually confirm or refute the matches you find.

5. Financial Reporting

Financial reports help you better understand and interpret your financial performance to make decisions. Be careful here: not every accounting software for ecommerce allows you to generate detailed financial reports. You may end up with an overly basic report, especially when using the free version of the software.

financial reporting from an accounting platform

6. Inventory Management

This accounting feature is useful for those ecommerce businesses who work with retail or distribution. You will be able to keep track of your stock and take inventory in your warehouses.

7. Tracking for Billable Hours & Project-Based Billing

Everything is simple here: if you work with clients on an hourly basis, keep track of the hours spent on the job and bill accordingly for the time spent. If you work from project to project, you can track tasks and budgets for your projects. It will be easier for you to bill clients for project costs at the end of the job.

8. Mobile Apps

Acccounting apps for ecommerce often do not replace the desctop program, but they can be helpful when you need the data ASAP. The capabilities of mobile versions of services can vary: some can only track expenses, while others have almost all the features of a desktop or web version.

Pricing of Ecommerce Accounting Software

Consider your business needs while choosing the software for ecommerce: for example, you might not need half of the paid version features, and then you should look for a cheaper program or even use the free version.

As a rule, there are two pricing models for accounting software: one-time purchase of a license or a month/quarter/year subscription. Subscriptions can cost from $10 per month for a basic plan and up to $60 per month for advanced functionality.

The price can also be affected by the number of users of the program, the number of businesses you want to connect to it, and the volume of transactions performed. It would be best if you also watched closely for so-called hidden fees: the price of a dollar or two for some small feature that is rarely needed.

It never hurts to study the trial version: that way, you can test different solutions and understand which business accounting software offers the most convenient scheme for you.

Top 10 Accounting Software for Ecommerce

The market offers many products for ecommerce accounting: from simple, free programs for calculating taxes and filling out tax returns to entire ERP systems for automating all of a company's business processes. We have made a review of the 10 best accounting software programs for ecommerce, in our opinion.

1. Intuit QuickBooks Online

QuickBooks is a web-based accounting automation service for small ecommerce businesses. It's a tool for those who want to save time by simplifying accounting and an integrated financial system. QuickBooks allows you to work with a group of up to five users. QuickBooks features:

  1. Tracking sales and expenses;
  2. Exchanging documents between devices;
  3. Check printing;
  4. Payment tracking;
  5. Online banking;
  6. Creating financial estimates;
  7. Exporting data to Excel;
  8. Working from mobile devices;
  9. Dashboards and feeds;
  10. Banking Data Synchronization;
  11. Automatic tax calculations;
  12. Balance sheets.

QuickBooks offers several rates to choose from. On the plus side, you can customize your plan. For example, there is the Independent Contractor Package, which costs $9.99 a month. Of the basic bundles, there is the Simple Starter Package, which costs $12.95 per month, the Basic Package, which costs $26.95 per month, and the Plus Package, which costs $29.95 per month. All plans can be used for free for 30 days.

2. Zoho Books

Zoho Books is a service for ecommerce accounting and managing finances, bills, banking services, and mobile control. It helps manage customers, capture incoming data, automate bill repeats, remind payments and send payment letters. Allows you to get money faster with payment gateways. Zoho Books will track expenses and cash outflows, as well as reimbursements, outstanding balances, and other situations. Key features of Zoho Books:

  1. Schedule disbursements and receipts;
  2. Management Accounting by Entity;
  3. Management accounting for multiple accounts;
  4. Auto-recognition of transactions;
  5. Support of different currencies;
  6. Financial analytics on projects;
  7. Analysis of expenses and revenues by item;
  8. Plan/actual analysis by line item.

Zoho Books has three pricing plans. The basic plan is $9 per month or $90 per year. It supports one user (and an accountant) and allows you to add 50 contacts to the system. The standard plan costs $19 per month or $190 per year. The Professional Plan costs $29 per month or $290 per year. Zoho Books also has additional fees for individual features, such as adding additional users or scanning documents.

3. FreshBooks Accounting Software

FreshBooks is a system for automating billing, changing invoices with a simpler interface compared to QuickBooks. With this service, you can send and manage ecommerce invoices much faster and collect all payments in one interface. At the same time, the platform supports credit cards, Google Checkout, and PayPal. The main features of FreshBooks:

  1. Online account management;
  2. Time tracking and filters;
  3. Recurring invoices and auto-pay;
  4. Team scheduling;
  5. Payment deadline reminders;
  6. Expense tracking;
  7. Accounting records and taxes;
  8. Automatic import of expenses;
  9. Mobile applications;
  10. Expense file attachments (PDF or images);
  11. Export to QuickBooks Desktop;
  12. Reports;
  13. Accounts receivable;
  14. Integration with 70+ cloud partners.

As with most accounting software, FreshBooks offers three rates. Lite costs $15 per month, Plus costs $25 per month, and Premium costs $50 per month. A feature of FreshBooks is the customizable Select plan. Here you can customize the functionality to suit you, and the price will also be calculated individually. You will need to contact the company for an individual quote. An account manager will also be assigned to you.

4. Xero

If you are just starting to explore accounting software for ecommerce, you will undoubtedly see the name Xero. The app allows you to accept payments, manage contacts, control inventory, pay bills, create purchase orders, track schedules, and more. The main functions of Xero:

  1. Automatic data entry;
  2. Secure communication with the bank;
  3. Bank reconciliation;
  4. Online invoicing;
  5. Automatic financial reporting;
  6. Company dashboard;
  7. Integration;
  8. Payroll.

This program has three plans - Starter for $9 a month, Standard for $30 a month, and Premium for $70 a month. For those who only need to send a few invoices a month, a starter plan is enough. It limits you to five accounts and/or offers five accounts and 20 reconciled bank transactions. Standard and Premium plans offer unlimited accounts, bills, and reconciliations. Premium is the only plan that supports multiple currencies.

5. Wave Financial

Wave is a double-entry bookkeeping site best suited for  independent contractors. It's free if you don't sign up for client payments or payroll. Some of Wave's main features include the following:

  1. Company dashboard;
  2. Customizable Accounts;
  3. Monthly bookkeeping;
  4. Integration with third-party services;
  5. Reports;
  6. Mobile app;
  7. Record templates;
  8. Transaction tracking.

Wave is a completely free service; you only pay to add additional features. For example, credit card processing costs 2.9 percent plus 30 cents per transaction, and you pay 1 percent for bank payments.

6. Sage 50 Cloud

Sage 50 Cloud is a massive small business accounting application designed for desktop use. The feature that makes it stand out from its competitors is its Microsoft 365 integration. Sage 50 Cloud is best suited for ecommerce companies that do not give up desktop software and whose employees work remotely but need access to some of the software's data. The main features are:

  1. Full accounts payable and receivable;
  2. Inventory management;
  3. Integrated payroll;
  4. Reports;
  5. Audit trail;
  6. Advanced budgeting;
  7. Job costing;
  8. Multi-company access;
  9. Role-based security;
  10. Industry-specific support.

All Sage 50 Cloud plans are based on a 12-month subscription to Sage Business Care, which automatically renews annually. Pro Accounting starts at $567 per year for a single user. Premium starts at $850 per year for a single user, and Quantum Accounting starts at $1,404 per year for a single user. Integration with Microsoft 365 is paid for separately.

7. GoDaddy Bookkeeping

GoDaddy mainly includes billing tools. In addition, this accounting service for ecommerce can integrate with eBay, Etsy, and Amazon. This is a great feature if want to tie your sales on these platforms to your accounting system. However, many features are missing from GoDaddy: for example, there is no support for multiple transaction types, no inventory management, and no project tracking or invoice payments. Still, GoDaddy includes the following features:

  1. Customizable reporting categories;
  2. Transaction tracking;
  3. Schedule C worksheet with tax-line assignments;
  4. Reports categorization;
  5. Tracking for billable hours;
  6. Dashboard;
  7. Client and item records;
  8. Contact templates generation;
  9. Invoice creation and sending;
  10. Time tracking;
  11. Mobile apps;
  12. Amazon, eBay, and Etsy connection.

There are also three types of rates here. The Get Paid plan, the easiest, costs $4.99 a month. The Essentials plan costs $9.99 a month, and the Premium plan costs $14.99 a month.

8. Sunrise

Sunrise has many ecommerce features. For example, this accounting platform can keep track of suppliers and products, create invoices, keep track of expenses, and import data from financial institutions. The program recently added integration with Gusto and Zapier payment systems. Other features of Sunrise include the following:

  1. Customizable invoices;
  2. Linking to a personal bank account;
  3. Multiple users access;
  4. Reports;
  5. Tax tracking;
  6. Invoices & recurring invoices;
  7. Building records;
  8. Expense tracking;
  9. Payment reminders;
  10. Mobile app;
  11. Multi-Currency;
  12. Integrations with Zapier and Gusto.

Sunrise is completely free to use. You only have to pay to integrate with Gusto or to accept payments through the processor. In addition, the service offers professional accounting services in three tiers. For $149 a month, the pro will provide up to 120 reconciliations; for $299 a month, you get up to 200 reconciliations; for $499 a month, you get up to 500 reconciliations.

9. Plooto

Plooto allows you to manage payments online and can also integrate with Quickbooks and Xero. This program is great for mid-sized ecommerce businesses or small businesses. It can also be useful for freelancers to send invoices and get paid quickly. There are some interesting features of Plooto:

  1. Digital Approvals (Desktop & Mobile);
  2. Fraud Detection;
  3. Automated Workflows;
  4. Electronic Payments (Accounts Payable & Accounts Receivable);
  5. International Payments (Multiple Currencies Available);
  6. Check Payments;
  7. Xero & QuickBooks Integration;
  8. Audit Trails and Record-Keeping.

Plooto offers a free monthly trial with all features available. The overall cost for a monthly subscription is $25.

10. Kashoo

Kashoo works on a double-entry basis and tracks income and expenses pretty well, as well as providing a project-by-project expense tracking feature. This service is best suited for a very small ecommerce business, with one or two employees at most. There are several features in Kashoo:

  1. Double Entry;
  2. Mobile Access;
  3. Payroll;
  4. Training Available;
  5. Multi-Currency;
  6. Live Support;
  7. Project costs tracking;
  8. Record templates for customers, suppliers, and inventory;
  9. Transaction forms for invoices and other income, invoices, and other expenses;
  10. Pre-prepared reports.

Kashoo costs $19.95 a month. For that money, you can manage your income and expenses while complying with double-entry bookkeeping rules.


Accounting software is a very good way to increase the productivity of an ecommerce company of any scale, even a startup. A good choice will make your life easier and will allow you to focus more on other essential business needs.

Before you choose accounting software for an ecommerce business, it is better to get familiar with its functions and make sure it is a good fit for you. Virtually every accounting software in our review has a free trial period that will allow you to take a good look around before making any monetary decisions.

However, it is worth remembering that the most important factor is ease and simplicity of use, as you will have to work with this program every day. We hope that our review will help you make your choice and simplify your ecommerce accounting.

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