Best Accounting and Invoicing Software for eCommerce in 2021
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Best Accounting and Invoicing Software for eCommerce in 2021

To avoid time-consuming repeated entries & inevitable mistakes, the best eCommerce software must interface with the e-commerce platform. Inventory & sales changes made in your eCommerce platform should be automatically transferred to your accounting software & vice versa. For an eCommerce business, here are the best accounting software options:


FreshBooks comes with excellent eCommerce integrations, with OneSaas, a third-party adapter that can connect to WooCommerce, Shopify, eBay, Squarespace, Wix, & Amazon. However, the service invoice template, like Xero, cannot calculate a sales tax based on a customer’s address or submit a sales tax return. FreshBooks also has limited inventory accounting capabilities, as it does not track amounts or calculate cost per unit. Therefore, FreshBooks is only recommended if you have little inventory or your e-commerce platform tracks your merchandiser’s price per unit.


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


  • There were no drawbacks discovered.


Numerous third-party connectors are available for QuickBooks Online, resulting in a seemingly unending range of possible integrations. However, QuickBooks Connect, which can be utilized rather than a third-party connector & is open for new subscribers, is pricey.


  • Shopify & WooCommerce have direct connectors.
  • Significant additional integrations with QuickBooks Commerce are available for a price.
  • Webgility, Connex, OneSaas, and Primaseller are some of the eCommerce 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 Commerce seems to be more expensive compared to third-party connectors of equivalent quality.
  • For present QuickBooks subscribers, QuickBooks Commerce has not yet been available.


Its inventory management & eCommerce interfaces are comparable to QuickBooks, although its management of state taxes is a touch weak. You can manually apply an endless amount of taxing authorities & sales tax rates on sales, which may be countless.


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


  • Each site with a chargeable sale must manually put up sales tax rates.
  • I’m unable to file sales tax returns.
  • Shopify does not have a direct integration.

Zoho Books

No eCommerce systems are natively integrated with Zoho Books. You’ll have to subscribe to either Zoho Inventory (beginning at $49 per month for more than 25 orders) or Kloud Connectors (starting at $30 per month for more than 25 orders) for any eCommerce integration. The advantage of using Zoho Books is the seamless connectivity with over 40 other Zoho applications that can manage your entire business, including CRM, sales, marketing, inventory, team communications, and employee recruiting.


  • Integrates with other Zoho apps to provide you with a full array of management tools.
  • Kloud Connectors, a third-party connector, is integrated.
  • Shopify, eBay, Etsy, & Amazon are all easily integrated with Zoho Inventory.


  • There will be no e-commerce integrations unless you subscribe to Zoho Inventory or Kloud Connectors.
  • There is no integration with well-known websites. For example, Squarespace and Wix are two of the most popular website builders.
  • It is impossible to establish the sales tax rate for each site or file sales tax returns.


Wave has a Zapier integration, allowing you to establish Zaps among Wave & various eCommerce platforms. However, because you’ll need to construct a Zap for each activity you wish to synchronize, this isn’t the same as simple integration. For example, you might use a Zap to automatically record an invoice or receipts in Wave whenever a sale is made on your e-commerce platform.


  • Forever free
  • Zapier integration is available.
  • Good basic accounting features


  • There are no third-party connections or direct e-commerce connections.
  • Inventory accounting is limited.
  • It is impossible to establish the sales tax rate for each site or file sales tax returns.


To eliminate excessive data entry and errors, ecommerce businesses should invest in accounting software that interfaces with their e – commerce platform. Because of its excellent integration, we suggest FreshBooks Online with most online enterprises.

Best Accounting and Invoicing Software for eCommerce in 2021

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