Best Accounting Software for Ecommerce Business

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What is ecommerce accounting software?  Do I need an accountant for my online retail business?  These are the questions that are asked by online retailers every day. If you are an established ecommerce retailer or an aspiring entrepreneur, understanding your accounting requirements for your ecommerce venture is very important. Accountants help to make the process hassle-free by handling all the financial transactions, especially in areas where self-management is not feasible.

Want to learn about ecommerce accounting software? Or accounting for small ecommerce business? Check out these free accounting software for retail business. Some ecommerce software can be a little complex, so before choosing


Accounting Software For Small Business — Online Accounting

QuickBooks has stood for a very long time as an overall solution for managing cash flow and taxes. Over the years, it has developed an interface that is much easier to use than much of the competition. Quickbooks has also integrated with all kinds of third-party tools to make it easy for you to utilize QuickBooks in your ecommerce store. 

QuickBooks online has options for businesses of all sizes, which makes it a good option if you want easy software to help you scale. Choose from options online to make your accounting easy wherever you are or a desktop option to keep things as secure as possible. 

Always a first choice for the self-employed, QuickBooks makes it easy to manage expense tracking, balance sheets, invoicing, inventory tracking, and a range of business essentials all-in-one place. Options start beneath $30 a month to give you all kinds of accounting solution functions like tracking income, billing, running reports, and allowing up to two accountants to access the account. If you want to scale up, pay more for accounts that cover more of what you need. Quickbooks has been the standard for a long time for good reason. For many small businesses with plans to grow, Quickbooks is the ultimate solution at a great price. 


Free Small Business Accounting Software Wave Financial

Wave accounting software lets you connect as many credit card and bank accounts as you want, making it much easier to keep track of all of your finances. Income and expense tracking is easy and free. You can take care of invoicing and scan receipts without any charges. 

For your customers to pay through your invoices directly, you’ll have to pay a percentage. If you want payroll to go through Wave, you’ll pay for this as well. Wave integrates directly with Shopify.

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Accounting Software Do Beautiful Business Xero Us

Xero has been giving QuickBooks a run for their money over the past couple of years, with a few features that may be a tremendous benefit for your company, depending on your needs. Xero offers three plans to help you scale from small business up to mid-size and even into a larger company. 

Even in the more affordable plans you can still have unlimited users, so if you want great collaboration between departments, this might be the best software for your needs. Live bank feeds enable constant bank reconciliation so you can see exactly how much money you have at any given second. 

As you go into the higher-paying plans, there are fewer restrictions on how much invoicing and how many quotes you can produce. Higher paying plans also feature support for various currencies. If you have no intention to scale up, this might not be the best company for you, as it is not ideal for small businesses unless you want to grow. 


FreeAgent is a cloud-based accounting solution for small businesses owners to manage invoices, expenses, payroll, tax returns and other accounting tasks.

FreeAgent Features

  • Estimates and invoices
  • Expense, income, and profitability reporting
  • Time tracking
  • Reporting dashboard for taxes, expenses, and more
  • Bank connections for transaction imports

FreeAgent Pros

  • Easy to use 
  • Free pricing plan available
  • Regularly updates with new features
  • Excellent tax reporting features

FreeAgent Cons

  • Pricier than other competitors
  • More template options needed
  • Lack of 24/7 support


FreshBooks Features

  • Customizable invoices
  • Payment reminders
  • Automatic late fees
  • Credit card processing
  • Add discounts to invoices
  • And more 

FreshBooks Pros

  • Easy to use 
  • Integrates with most ecommerce platforms
  • Constantly updates with new features
  • Detailed help articles for self-service support
  • Simple pricing structure

FreshBooks Cons

  • Limited inventory tracking
  • Only supports single-entry accounting
  • Reporting features are lacking when compared to other software


Designed for large enterprises, NetSuite cloud financials and accounting software helps finance leaders design, transform, and streamline their processes and operations. 

NetSuite combines core finance and accounting functions with strong compliance management. This combination improves business performance and increases financial close efficiency while reducing back-office costs. 

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If you are running a large business with worldwide operations, NetSuite is worth checking out.

NetSuite Features

  • Billing 
  • Revenue recognition
  • Planning and budgeting
  • Global accounting
  • Sales order management
  • Returns management
  • Inbound and outbound logistics

NetSuite Pros

  • Leading software for large enterprises
  • Offers many features not available with other accounting software
  • Support for global accounting if you operate in multiple countries
  • Offers compliance services to support ASC 606, GAAP, SOX, and others

NetSuite Cons

  • Not a good solution for small- to medium-sized businesses due to pricing
  • Multiple NetSuite software products are required if you want all their features

Sage Accounting

Sage is a cloud-based accounting and invoice management solution for small businesses. It offers core accounting, project accounting, expense management, and compliance management all in one.

Sage manages all the documentation and processes required in business payments such as price quotes, estimates, statements and invoices. They offer integration with major banks, allowing users to import all payment transactions automatically. 

All information is available in a single dashboard, which allows users to stay up to date on their cash flow and pending payments.

Sage Accounting Features

  • Inventory/stock management
  • Bank reconciliation
  • Automated billing
  • Forecasting
  • Pay bills electronically, print paper checks
  • Supplier management

Sage Accounting Pros

  • Easy to use 
  • Connects to all major banks for automatic transaction updates
  • Automates basic tasks including reconciliations
  • Can email everything to customers to reduce physical paperwork
  • Supports inventory and stock management tracking

Sage Accounting Cons

  • Web app has less features than desktop app
  • Occasionally slow even with a good internet connection
  • If using the desktop app, you must create backups or you risk losing data

Zoho Books


  • Integrates with other Zoho apps to provide a complete suite of management software
  • Integrates with third-party connector Kloud Connectors
  • Zoho Inventory integrates directly with eBay, Shopify, Etsy, and Amazon


  • No ecommerce integrations without subscribing to either Zoho Inventory or Kloud Connectors
  • No integration with popular sites Squarespace and Wix
  • Cannot determine sales tax rate by location or file sales tax returns

Zoho Books does not directly integrate with any ecommerce platforms. You’ll need to subscribe to either Zoho Inventory, starting at $49 per month for more than 25 orders, or Kloud Connectors for $30 per month for each ecommerce integration. The benefit of choosing Zoho Books is the seamless integration with more than 40 other Zoho applications that can manage your entire business, including customer relationship management (CRM), sales, marketing, inventory, team communications, and employee recruitment.

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Zoho Pricing

  • Zoho Books Basic: $9 per month for two users and 50 customers and vendors
  • Zoho Books Standard: $19 per month for three users and 500 customers and vendors
  • Zoho Books Professional: $29 per month for 10 users and unlimited customers and vendors
  • Zoho One including 40+ Zoho Apps:
  • $35 per employee per month, or
  • $90 per user per month

Zoho offers a 14-day free trial for new customers.

Sage 50cloud

Sage 50cloud Accounting Sage Us

If you want a complete accounting solution for your small business that can keep up with you as you grow and you’re willing to pay some of the higher prices in the business, this might be the right solution for you. Despite its name, Sage 50cloud does not have to be exclusively on the cloud. Hard-drive based software integrates with the cloud so that you can get the reports you want where you need them without opening up all your finances to the cloud. 

If you have a lot of inventory to manage, Sage may have even more value for you, since they offer some of the best tools available for inventory tracking. This makes it a great option for ecommerce businesses with plans to grow big. Sage is an excellent option for anyone with employees who work remotely. 

The interface on Sage is not as easy to use as some of its competitors, with awkward traits like links opening its new windows and a busy interface. The lack of a good mobile app is a big problem for many small businesses. However, this software offers customizability, good invoicing, and in-depth records that more than make up for a bit of clumsiness for many business owners. 


Hiring a bookkeeper onsite may be your first reaction if you’re running a small to medium-sized business, but using the best accounting software for ecommerce business is something you should consider as well. These are some great programs that will help you manage the financial side of your ecommerce business and save you time and money as well.

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