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The Best Bookkeeping Software for eCommerce Merchants

Are you on top of your finances?

If not, you aren't alone. Bookkeeping is probably the last thing we want to do as eCommerce merchants. But for merchants looking to scale, having the right bookkeeping software is non-negotiable.

In other words, you can't run your business out of Excel forever.

If your online business is hitting a wall due to bookkeeping difficulties, you need this list of the best accounting software for eCommerce sellers.



Below, you'll find our favorite bookkeeping services -- and the pros and cons of each -- so you can choose the most appropriate bookkeeping solution for your online business.


1. QuickBooks: Grow Up and Become an Enterprise



There's a reason that QuickBooks is the gold standard for small business owners, professional CPAs, freelancers, and enterprise-grade companies. It's a powerful bookkeeping platform that you can quickly set up to manage your books, invoices, accounting. It also integrates with a host of other applications.

Quickbooks' best features include:

  • mobile access
  • payroll processing
  • receipt capturing and organizing
  • PayPal and Shopify compatibility
  • support for multiple users
  • income and expense tracking
  • sales and sales tax tracking
  • invoice and payment tools


QuickBooks can scale and grow with any size company, but it's great for small online businesses because it's so easy to use. It offers advanced business reporting metrics through an easy-to-configure dashboard. And as a flagship bookkeeping solution, QuickBooks constantly revises and upgrades their platform to keep it up to speed with the latest software trends.

It's been around for a very long time, so most business applications are eager to integrate their solutions with it. That makes QuickBooks one of the most compatible bookkeeping tools available for businesses.

So what's the catch?

If the task involves accounting and bookkeeping, QuickBooks can do it better than most competing platforms. But QuickBooks is designed for U.S.-based businesses only.

And although QuickBooks' pricing is competitive and you definitely receive a quality solution, it is pricier than competing platforms. A basic small business subscription costs between $12 and $40 per month. Scaling up for more business reporting features can cost between $70 and $150 per month. Enterprise versions of the software must be negotiated with a sales associate.


2. Xero: Explore Global Business Opportunities



Xero provides all of the bookkeeping features you want, along with some new technology that eases the burden of reconciling bank transactions.

Xero's new bookkeeping tech includes:

  • inventory tracking tools
  • bank transaction reconciliation
  • invoice sending and tracking
  • multi-currency transactions
  • over 800 business application integrations
  • direct connections to your bank
  • a reputation for stellar online support
  • bill pay management tools
  • mobile app access
  • sales tax tools


Xero makes it easy to connect and collaborate in the cloud. It includes a variety of apps and integrations, comes mobile-ready, and offers multi-currency support for global businesses.

What are the cons?

The cons of Xero include limited features in the basic plan. Although a low-price, entry-level subscription is available for $9 per month, many of its best features -- such as multi-currency and global business support -- aren't available at that price point. The basic plan also limits you to sending only five invoices and 20 bank reconciliations per month.

The premium for the full range of Xero services is $60 per month.


3. Zoho: Your All-in-One Business Bookkeeping Solution




Zoho offers a suite of bookkeeping tools for businesses of all sizes. Zoho Books is the low-cost, cloud-based bookkeeping software for small businesses. As your online business expands you can easily build out to include more sophisticated Zoho tools, such as Zoho CRM or the all-inclusive Zoho One platform.

Zoho's best features include:

  • easy invoice creation and management and invoice templates
  • mobile-ready software that can be accessed from anywhere
  • the ability to send reminders
  • multiple payment options and payment gateways for customers
  • expense receipts uploading
  • bank transaction reconciliations
  • multi-language support
  • stripe integrations
  • customer and supplier contact management


Zoho's flexible pricing options include the lightweight Zoho Books at $9 per month. The professional edition costs $29 per month. Zoho One costs $30 per employee via the employee-pricing model or $75 per user via the flexible-user-pricing model.

Zoho's payment gateways make it easier than ever for your customers to pay for products and services, and its automatic payment reminders keep you from missing your payments.

Here's the deal - there are two cons with Zoho worth noting.

  1. There are limited features in Zoho's basic plan which only allow you to manage 50 contacts.
  2. Only the most expensive version of Zoho includes sales orders, purchase orders, and inventory tracking.


Which Bookkeeping Software Should Your eCommerce Business Use?

These are the creme-de-la-creme of bookkeeping solutions for online businesses. They are designed to serve the needs of eCommerce merchants -- especially those that hope to scale and grow.

Which bookkeeping solution should you use?

Here's our advice -

  • QuickBooks is our choice for eCommerce business accounting, simply because it has the might and reputation to service your needs, whether you’re a one-man mechanic shop or a large-scale enterprise.
  • If you plan to build an international business, you might want to go with Xero, which offers multi-currency and international business support.
  • If you want an all-in-one, accounting, CRM, and business analytics platform, Zoho One has some impressive, all-inclusive offerings.


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Fascinated by emerging technologies and the laws and market trends that follow them, Jeremy Hillpot has a background in consumer-investor fraud litigation, marketing, and technology, which provides a unique perspective on a vast array of topics including eCommerce, website tech, investments, startups, cryptocurrencies, and the law. Contact Jeremy at

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