7 Best Ecommerce Accounting Software In 2021

Accounting Software

To avoid time-consuming repeated entries & inevitable errors, you must need the best eCommerce platform. Inventory and marketing changes made in your e-commerce platform should be automatically transferred to the accounting software & vice versa. For your eCommerce site, here are 7 of the top accounting applications available:


OneSaas, a third-party adapter that can connect to Shopify, WooCommerce, Squarespace, Wix, eBay, and Amazon, is one of FreshBooks’ decent e-commerce integrations. FreshBooks, like Xero, is unable to calculate a sales tax depending on a customer’s postcode or file a sales tax return. FreshBooks also has limited inventory accounting capabilities, as it does not record quantities or estimate cost per unit. FreshBooks is only recommended if you have little stock or if your e-commerce platform tracks your merchandiser’s cost per unit.


  • Shopify & Squarespace have direct connectors.
  • Integrate with OneSaas, a third-party adapter.
  • Telephone customer service is excellent.


  • The quantity of billable clients is limited in these plans.
  • Accounting for inventory is extremely limited.
  • It is not possible to establish the sales tax rate for each site or to file sales tax returns.

Zoho Books

No e-commerce systems are natively integrated with Zoho Books. For any e-commerce integration, you’ll need to enrol to either Zoho Inventory (beginning at $49 per month for more than 25 orders) or Kloud Connectors (starting at $30 per month for further than 25 orders). The advantage of using Zoho Books is the seamless connectivity with over 40 other Zoho apps that can handle your complete business, including CRM, sales, advertising, inventory, group communications, and employee recruiting.


  • Works with the other Zoho apps to give you a full suite of software solutions.
  • Cloud Connections, a third-party connector, is integrated.
  • eBay, Shopify, Etsy, & Amazon are all easily integrated with Zoho Inventory.


  • There will be no e-commerce integrations unless you subscribe to Zoho Inventory with Kloud Connectors.
  • There is no integration with well-known websites. Squarespace & Wix are two of the most popular website builders.
  • It is not possible to establish the sales tax rate for each site or to file sales tax records.


Ecommerce businesses, unlike certain industries with basic accounting, should not compromise on their accounting system. Online payments, multichannel retail, inventory control, & sales tax are just a few of the aspects that make e-commerce accounting difficult and justify the investment in QuickBooks Online or Xero. Wave, on the other hand, is the ideal option if you insist on using free accounting software.


  • It’s totally free, and it works with Zapier.
  • Basic financial features that are good


  • There are no third-party connections or direct e-commerce connections.
  • Inventory accounting is limited.
  • It is not possible to establish the sales tax rate for each site or to file sales tax records.


Because of QuickBooks’ dominance in the small business accounting sector, practically all online stores will make every effort to ensure that their interfaces are smooth and simple. Many third-party connectors are available for QuickBooks Online, resulting in a seemingly unending range of possible integrations. QuickBooks Connect, which can be utilized than a third-party connection and is receptive to potential subscribers, is pricey.


  • Shopify & WooCommerce have direct connectors.
  • Significant additional integrations with QuickBooks Commerce are available for a price.
  • Webgility, OneSaas, Connex, & Primaseller are some of the e-commerce programs you can use.
  • Sales tax is automatically calculated and filed based on the customer’s location.


  • It’s more pricey than alternative accounting software for small businesses.
  • QuickBooks Business is more costly than third-party connectors of equivalent quality.
  • For present QuickBooks users, QuickBooks Ecommerce is not yet accessible.


Xero is a wonderful alternative for e-commerce businesses that don’t want to utilize QuickBooks. Its inventory accounting & e-commerce interfaces are comparable to QuickBooks, although its management of sales tax is a touch weak. You can manually apply an endless amount of taxing jurisdictions & sales tax levels on sales, which may be countless.


  • WooCommerce & BigCommerce have direct integrations.
  • Webgility, OneSaas, A2X, & Parex Bridge are examples of third-party adapters.
  • Inventory management that works
  • Much less expensive than QuickBooks, as well as all options include unlimited employees.


  • Each site with a chargeable sale must individually put up sales taxation rates.
  • You may unable to file sales tax returns.
  • Shopify does not have a deep interface.


FreeAgent is a cloud-based accountancy service that helps small business owners handle invoicing, spending, payroll, tax returns, as well as other financial chores.


  • Simple to use
  • There is a no-cost price option available.
  • New features are added on a regular basis.
  • Features for tax reporting that are excellent


  • Expenses are higher than those of competitors.
  • More template choices are required.
  • Lack of round-the-clock assistance


NetSuite cloud financials & accounting software, designed for large businesses, assist finance leaders in designing, transforming, and streamlining their procedures and operations. NetSuite brings together fundamental finance and accounting processes with robust compliance management. The combination boosts corporate performance & enhances financial closing efficiency while cutting back on back-office expenses.


  • Exceptional software for large businesses
  • Many features not found in other online accounting Global accounting support if you run in multiple countries
  • Provides ASC 606, GAAP, SOX, as well as other compliance services.


  • Due to pricing, this is not an appropriate choice for small to medium-sized organizations.
  • If you want to use all of NetSuite’s functionality, you’ll need multiple software solutions.


To eliminate excessive data entry and errors, e-commerce businesses should invest in the best small business accounting software that interfaces with their e-commerce platform. With most e-commerce firms, We recommend FreshBooks Online. Although it has become less expensive than QuickBooks, it does require the use of sales-tax plugins, such as Avalara, to give the same level of sales tax simplicity.