As your ecommerce business scales, so does the complexity of your finances. Manual spreadsheets, CSV exports, and piecemeal tracking may work in the earliest days — but beyond a certain point, they become a time bomb. In fact, many accountants will tell you: once you hit 500–1,000 orders per month or start selling across multiple channels/states, you must upgrade to software. At that point, automation, error reduction, and clean reporting become critical.
Among the top options, QuickBooks and Xero often emerge as the most recommended by accountants — due to ecosystem support, integrations, and familiarity in the accounting world. But they’re not the only choices.
When Should I Start Using Accounting Software?
Many online sellers begin with Google Sheets or Excel, but as soon as your store starts getting real traction, manual tracking becomes risky.
Here’s when it’s time to switch to professional accounting software:
- You process hundreds of orders per month, especially across different marketplaces (Shopify, Amazon, TikTok Shop, eBay, etc.)
- You handle sales tax or VAT in multiple states or countries
- You track inventory, returns, or cost of goods sold (COGS)
- You notice marketplace payouts never match your bank deposits because of fees, refunds, and adjustments
- You work with a CPA or accountant who needs clear, accurate financials
- You want to prepare for investors, loans, or tax season with confidence
If any of this sounds familiar, it’s the right time. Accounting software automates your bookkeeping, saves hours of manual work, and keeps your numbers clean and reliable.
What CPAs and Accountants Recommend
Most accountants and CPAs agree on a few key points when it comes to choosing ecommerce accounting software:
- Automation saves money — The less you manually enter, the fewer errors you make.
- Integration matters — Software should connect with your sales channels like Shopify, Amazon, and WooCommerce.
- Accurate reconciliation is essential — Matching marketplace payouts to sales and fees can be tricky without automation.
- Inventory and COGS tracking — Knowing what products you sold, what they cost, and your real profit margin is key.
- Audit-ready reports — You want clean financial statements your CPA can trust.
That’s why most accountants recommend proven systems such as QuickBooks or Xero — because they integrate with popular ecommerce platforms, support automation, and are trusted worldwide.
Top Recommended Accounting Software for Ecommerce
QuickBooks Online
QuickBooks is the most widely used accounting software among small and medium ecommerce businesses.
It’s often the first choice for CPAs because it’s reliable, integrates with almost every ecommerce platform, and offers strong reporting tools.
Key features:
- Built-in integrations for some marketplaces
- Tracks income, expenses, and inventory
- Supports multiple users and accountant access
- Great for businesses processing from a few hundred to several thousand monthly orders
QuickBooks is ideal if you want an all-in-one solution and easy collaboration with your accountant.
Xero
Xero is another top choice, especially among accountants who prefer its clean interface and flexibility.
It offers unlimited users, excellent automation, and connects with hundreds of ecommerce apps and plugins.
Why CPAs recommend Xero:
- Clear dashboards and reports for tracking sales and cash flow
- Smooth integrations with ecommerce tools
- Scales well as your order volume grows
- Great collaboration features for teams and accountants
Xero is especially popular with businesses that want a modern, cloud-based system that’s easy to expand as they grow.
Other Recommended Tools
While QuickBooks and Xero dominate the CPA recommendations, there are other good options for certain sellers:
- Zoho Books – Affordable, well-integrated with other Zoho business tools.
- FreshBooks – Very user-friendly, great for service-based or simple ecommerce.
- Wave – Free option for very small sellers who just need the basics.
How GeekSeller Helps with Accounting Integration
At GeekSeller, we help ecommerce businesses send clean, structured data from marketplaces and ecommerce platforms like Walmart, Amazon, eBay, Woo, Shopify, BigCommerce, Shopify, and TikTok Shop directly to QuickBooks or Xero. This makes reconciliation easy and accurate — exactly how accountants and CPAs like it.
If you need help connecting your accounting software or setting up automation for your financial data, contact us anytime — our team can guide you through it step by step.
