Best Accounting Software for Ecommerce in 2021

If you are on the lookout for the best accounting software for ecommerce stores, you should know that there’s no “one size fits all” solution. With so many different accounting software solutions on the market, it can be a bit confusing to select the right one. For instance, a small business may not want to choose an expensive solution for sending invoices, as it could severely impair their profit margins.

Ecommerce business owners need to evaluate the pros and cons very carefully when selecting any accounting software solution. Of course, you will want basic features such as invoicing, inventory management, credit card charging facility, sales tax incorporation, and essential bookkeeping solutions.

If your ecommerce business doesn’t make it easy for clients to make payments, you’ll lose out on a significant amount of potential revenue. Thankfully, there are several integrated solutions that you can choose from.

The 7 Best Ecommerce Accounting Software

There are some software solutions that are more popular than others because of their feature set and pricing. Here are the 7 best accounting software solutions for ecommerce store owners.

QuickBooks Online

quickbooks online homepage - best accounting software

The Intuit QuickBooks is one of the most popular accounting software solutions for business owners. Designed primarily for small businesses, QuickBooks has everything that you could ask for, including a Shopify integration, a mobile app, and a fantastic online dashboard that gives you a comprehensive outlook of your company’s financial position. QuickBooks Payments is also a viable payment processor.

One of the reasons why so many businesses prefer QuickBooks Online is because of its ease of use. When you sign up, the program asks you a few questions about your business. It uses your answers to quickly set up a profile and modify some core settings in order to optimize the program based on your business type.

You can also import your accounting data from CSV or Excel files, along with all your product, vendor, and other associated profiles. However, this is a bit complicated, and you may need the help of an accountant to import the data.

The QuickBooks Dashboard gives you a simple overview of your account balances, including receivables, payables, expenses, and sales. It also provides quick links for invoicing, basic maintenance, and other activities, like viewing graphs of financial performance over specific periods.

QuickBooks is primarily designed for entrepreneurs with little to no accounting experience. However, there’s a bit of a learning curve involved. Important information, like cash flow data, bank account balances, and other inflows and outflows are also updated in real-time.

QuickBooks has an array of reporting and analytical tools that you can use in order to get a more comprehensive understanding of your store’s fiscal performance. You can view multi-channel sales data, and detailed supplier or vendor records. There are also individual templates available for inventory and non-inventory parts.

It is also a fantastic inventory management solution, allowing you to input your starting inventory. Then, QuickBooks will continue to track it, and will notify you when your inventory falls below a specific limit.

Pricing 💰

Quickbooks offers incredibly affordable plans, making it an incredibly affordable accounting solution for ecommerce stores. Pricing starts from $8 per month when paid annually, and maxes out at $17/month for the Plus package. For additional subscriptions, you need to contact their support.

Pros 👍

  • Offers support for numerous add-ons and integrations
  • Highly customizable reporting framework
  • Easy to set up
  • Excellent payroll support
  • Hybrid sales tax calculation

Cons 👎

  • Customer support isn’t the best
  • Mobile app functionality is limited
  • Dashboard may seem a bit cluttered to new users

FreshBooks

freshbooks homepage - best accounting software

FreshBooks is another fantastic accounting system that does the job of a digital bookkeeper and more. It is suitable for ecommerce platforms that need an all-in-one solution. It’s not just for ecommerce stores; freelancers, self-employed professionals, and even businesses with contractors can take advantage of its many features.

FreshBooks supports double-entry accounting, so you don’t have to worry about creating suspense accounts at the end of the year. More importantly, FreshBooks offers fantastic business data and insights that can help you make important decisions about your ecommerce business.

FreshBooks started off as a simple invoicing solution, but the company continued to add new features, and it eventually evolved into a full-fledged ecommerce accounting software solution. Because of its affordable pricing, it’s incredibly popular amongst startups and sole proprietors.

One of the best features of the program is automated bank reconciliation. The program automatically imports financial transactions and categorizes them, which simplifies bank reconciliations by a considerable margin.

The Credits feature is used to automate prepayments, credit notes, and overpayments. The Reports button on the dashboard also provides a range of financial reports, including cash flow movements, P & L, end-of-year reports, and a lot more.

Inventory tracking is also available, and it also supports third-party payment processors like PayPal.

Pricing 💰

The reason why FreshBooks is so popular is primarily because of its pricing. It starts from as little as $6 per month for the Lite package, and the most expensive variant costs $20 per month for unlimited billable clients. For enterprise needs, they also have custom packages available.

Pros 👍

  • Very streamlined UI
  • Lots of integrations
  • Functionality for making estimates and retainers
  • Automated mileage and expense tracking
  • Integrates well with marketplaces like Amazon and Etsy

Cons 👎

  • You can’t get quarterly tax calculations
  • Mobile app has severely limited functionality
  • Invoices can’t be customized fully

Xero

xero accounting homepage - best accounting software

Then, there’s Xero. Widely regarded as a versatile accounting program that is suitable for online business owners or freelancers, Xero has made a name for itself amongst other accounting software options by providing simplified functionality and affordable packages.

It offers mobile apps for both Android and iOS, and it’s an ideal choice for people who use multiple accounting tools, but want to bring everything under one roof. For online store owners, Xero offers a fantastic dashboard that gives you a comprehensive overview of your overall spending.

From balance sheets to P & L reports, Xero simplifies accounting by putting everything just one button away. It supports integration for popular platforms like Stripe, and uses double-entry bookkeeping.

One of the best things about Xero is that over the past year or so, the company has continued to add new features to the platform, including inventory tracking, expense management, and online payment functionality.

It also integrates with platforms like Bigcommerce very well for tracking bank transactions and other accounting tasks. If you sell on marketplaces like eBay, Xero Accounting might be just what you need.

For freelancers who need time tracking options, Xero Projects is another fantastic option. If your ecommerce business is focused on maximizing profitability, you can’t go wrong with Xero.

Pricing 💰

Compared to other options on this list, Xero is a bit more expensive. Packages start from $20/mo for the Starter package, and then there’s the Standard ($30) and finally, the Premium ($40) that unlocks full functionality. Xero also offers a free trial for 30 days, after which you can decide to choose the right package based on your needs.

Pros 👍

  • Extensive customization features
  • Project tracking options
  • Bank reconciliation options
  • Mobile access
  • Simplifies time-consuming tasks like preparing reports

Cons 👎

  • You can’t set reorder levels
  • Massive difference in terms of features between online and mobile app dashboards
  • Limited support via live chat or phone

👉 Read our comprehensive Xero review.

Wave Accounting

wave accounting homepage - best accounting software

Wave is a comprehensive small business accounting software solution that’s ideal for ecommerce store owners. If you want a comprehensive solution to streamline your financial accounting, tax returns, and invoicing, Wave is a great choice.

It’s the right accounting software for entrepreneurs that want granular control over their finances. The dashboard gives you detailed information about your expenses and your income and allows you to track payroll, invoicing, and prepayments through a centralized portal.

Wave allows you to create professional invoices at no extra charge, and it also syncs very efficiently with your Shopify store or your WooCommerce online store. Wave has two discrete product offerings; the accounting software and the invoicing solution.

When it comes to filing tax returns, Wave allows you to easily calculate your tax payable, and also gives you detailed insights into deferred tax liability or income. It’s designed to be an accountant-friendly cloud solution that seamlessly tracks your expenditure and income.

It uses 256 bit encryption, so you never have to worry about your financial information getting hacked or leaked. Since it uses double-entry accounting like several others on this list, your accountants will find it much easier to track payments through the program.

Pricing 💰

Here’s the best part: Wave Accounting is absolutely free. There’s no setup fee, no hidden charges, and no recurring fee that you have to worry about. This also includes unlimited bank and credit card transactions. Needless to say, Wave offers unparalleled value at no cost. You will have to pay for payments and payroll, however.

Pros 👍

  • Free to use
  • Uses double-entry accounting
  • A fantastic user interface
  • Support for multiple currencies

Cons 👎

  • Templates are fairly simple
  • The mobile app has limited features
  • You can’t offer discounts to customers through Wave
  • Time-tracking features are limited

👉  Read our Wave Accounting review.

Kashoo

kashoo accounting homepage - best accounting software

Kashoo is a fantastic ecommerce-centric accounting software solution that automates a large part of accounting tasks in smaller businesses. It automatically categorizes transactions and sorts them, which can save you a great deal of time and money.

Kashoo also has a Smart Inbox, which automatically keeps track of vendors that you normally do business with, and prioritizes their emails. Kashoo’s mobile app uses OCR technology to scan and create digital copies of receipts, and then automatically categorizes them.

This is important because you won’t have to worry about duplicate entries in your system. Kashoo also automatically categorizes payments in accounts mostly checked by the IRS and the CRA, so when the taxman comes calling, you don’t have to worry about paying more than your fair share.

Another fantastic feature that Kashoo offers is that it automatically creates contacts for every invoice recipient. It saves you the extra steps of importing or manually entering data.

Above all, Kashoo simplifies online payments and transactions by allowing users to accept payments from multiple sources. It’s powered by WePay, and reduces payment friction drastically. If you are a SaaS business, Kashoo is an excellent choice.

Pricing 💰

If you are a small-scale business, they have a free package that starts from $0 per month. Their accounting package starts from $20 per month, and the full offering costs $30. The free option is exclusively for invoicing, however.

Pros 👍

  • Constant updates
  • Decent for income and expense tracking
  • Free version for smaller businesses
  • Decent range of templates

Cons 👎

  • No conventional dashboard; everything’s divided by tabs
  • Android app still in development
  • Limited set of integrations

Zoho Books

zoho books homepage - best accounting software

The Zoho suite of software programs are designed for all kinds of businesses. They offer a range of productivity applications designed for marketers and business owners. Zoho Books, as you can imagine, is their financial services offering geared towards small businesses.

If you need a small business accounting solution, Zoho Books is definitely one of the best in the market. Business owners that already use Zoho in their ecommerce suite will find Zoho Books exceptionally easy to integrate in their platform.

It offers convenient facilities for payroll management, invoicing, billing, making estimates, expense tracking, and a lot more. If you want to automate workflows in your accounting department, Zoho Books is an excellent choice.

Zoho Books offers an end-to-end accounting solution, from tracking deals to sales orders, so you don’t have to worry about doing those time-consuming tasks on your own. That’s not all – Zoho Books also features convenient reporting tools that allow you to get a clear overview of how your business is doing.

Pricing 💰

For businesses generating less than $50k per annum, Zoho Books is free. Their Standard plan starts from $10/mo, with two other options priced at $20 and $30 per month. Add-ons are also available for separate branches and users.

Pros 👍

  • Support for all major payment gateways
  • Time tracking
  • Renowned in the business industry for their support offerings
  • Offers comprehensive form management and customization features

Cons 👎

  • Payroll features are not available globally, or across the full country
  • Integration options are limited

Sage Accounting

sage accounting homepage - best accounting software

Last but definitely not the least, there’s Sage Accounting. This is one of the most feature-rich solutions out there. For those who don’t know, Sage is one of the biggest names in the cloud accounting solutions industry.

If you are an accountant, you will find Sage considerably easy to understand. In many cases, Sage seems like an application that’s geared more towards accountants instead of small business owners.

There are certain features missing that you’d normally find in other programs, like time tracking or managing purchase orders. The moment you sign up, Sage gives you a series of signup tools that you can use to quickly set up your Sales and Expense options, as well as your tax returns settings.

The user experience is fairly simple and straightforward, and it uses double-entry bookkeeping (a win for accountants!). However, one thing that many people will notice about Sage is that the user interface seems slightly old when compared with other big names, like Zoho Books or QuickBooks.

Apart from that, Sage offers mobile apps for both iOS and Android, and both of these are relatively well-done. Import options are also extensive, allowing you to import CSV files supporting several types of data.

Pricing 💰

One of the biggest benefits of Sage is that it offers you 70% off for the first six months. The Start package begins from $10 per month, whereas the Sage Accounting package, which is generally $25 monthly, is discounted to $7.5 per month for the first six months.

Pros 👍

  • Very easy to set up
  • Simplistic interface
  • Offers project tracking options
  • Decent mobile apps available on both Android and iOS

Cons 👎

  • The interface looks old
  • No time tracking
  • Limited customization features for reports

What is Ecommerce Accounting Software?

Ecommerce store owners need a robust software program that is able to quickly adapt to their needs. They need an accounting solution that keeps track of inventory, vendor payments, and above all, sales.

Because ecommerce stores are mostly automated, deploying a software program is essential for making sure that all transactions are recorded. There are quite a few variable costs involved, so it’s important that you choose an accounting software program which offers a high degree of flexibility.

Ecommerce accounting software allows store owners to easily keep a track of all transactions that take place in the store. The software program should allow business owners to keep a check on available inventory, determine their cost of sales, overall profit margins, and other details, like tax payable, accounts receivables, as well as overhead expenditure.

Most ecommerce accounting software is cloud-based, you don’t have to worry about installing and saving data in your laptop or computer. This also means that you can access records from any device; you just need to log into the account in order to access the latest figures.

Almost every ecommerce accounting software solution provides a suite of solutions, ranging from simplified invoicing to customizable reporting. For every purchase made, the software should automatically generate an invoice for the customer.

Supplier tracking is also made convenient through these software programs, as they can be used to issue receipts to suppliers and to update inventory records.

What to Look For When Selecting an Accounting Software for Ecommerce Businesses

As you can see, there are plenty of choices available for people looking for a decent accounting software for ecommerce businesses. However, you can narrow down your choices if you know what you are looking for. Ideally, here are some key features to look for in any accounting software for ecommerce store owners.

Reports

Any program you choose should have a reporting feature that generates different reports at the touch of a button. This involves basic financial statements including the statement of financial position, the statement of profit and loss, and statement of cash flows.

More importantly, the program should feature extensive data visualization options. From pie charts to bar graphs, users should have the freedom to manipulate the data however they see fit in order to get a clear picture of where their store stands.

Security

The software program should be secure enough to protect all your sensitive data. Ideally, the accounting solution you use should feature 256-bit encryption and two factor authentication, so that only authorized individuals are able to access the dashboard. Security is a key concern for most business owners, especially because all sensitive information is stored in the cloud.

If the software program does not feature robust security, anyone with a bit of technical knowledge and access to brute force tools can hack into the system.

Integrations

More importantly, you will want to choose an accounting software program that integrates seamlessly with other programs you have deployed on your store. For instance, if your store is based on Shopify or WooCommerce, the accounting software program should integrate seamlessly to track payments and invoices.

Almost all major software programs provide integrations and add-ons that maximize functionality and make it easy for you to run your store through a centralized platform. Collaboration between different departments such as inventory and payroll is very important.

Robust Support and Updates

The program you choose should also feature consistent updates and support features. The team should work actively to add new features into the program in order to streamline its performance.

More importantly, they should also take support seriously. In case you have a question, you should have multiple support options available, such as a live chat solution, email, or phone. This instills confidence in the user and shows that the team really cares about their product.

The Bottom Line

Using a decent accounting store for ecommerce store owners is essential now. You don’t want to be scrambling at the last minute when the time for taxes is due. It’s always a wise idea to make sure that you have all reports available when needed. A decent accounting software program will do just that, so choose from any of these seven great options!

Najam Ahmed

Najam Ahmed is an experienced content marketer and copywriter with a focus on SaaS offerings, startups, digital agencies, and ecommerce businesses. He’s worked closely with founders and digital marketers over the past eight years to produce articles, eBooks, newsletters, and guides. His interests include gaming, traveling, and reading.