Shopify Bookkeeping & Accounting Tiers Explained

Bookkeeping is one of those things most Shopify store owners ignore until it becomes a problem. Whether you’re tracking orders manually or using full accounting software, understanding where you are in your business journey helps you choose the right system. In this post, we’ll break down four bookkeeping tiers that grow with your Shopify store — from free Excel sheets to one-on-one accounting with Bench.

Tier 1 – Just Starting Out (Excel or Google Sheets)

When I launched my first Shopify store, I had no sales and no budget for tools. My bookkeeping method? A simple Excel file. Using cash-based accounting (logging income and expenses as they happen) or accrual accounting (tracking inventory and owed money) gives you a basic financial picture. This method is completely free, which is perfect when you’re just getting started. You can even find Shopify Excel bookkeeping templates online for free.

Tier 2 – Sales Are Coming In (Wave Apps)

Once I started getting regular orders, I switched to Wave Apps — a free accounting software that helps automate simple tracking and invoicing. Wave connects to your business bank account and creates a more professional record of income and expenses without adding cost. It’s a great fit for merchants surviving their first Shopify year while keeping expenses low. If you’re at this stage, consider joining the 30-Day Beginner’s Shopify Program to strengthen your store’s foundation as you grow.

Tier 3 – Scaling and Profitable (QuickBooks, Xero, FreshBooks)

As your store scales, free software might not cut it anymore. Tools like QuickBooks, Xero, or FreshBooks integrate directly with Shopify and offer full-featured reporting, automation, and tax-ready data. Though these have a monthly cost, they often reduce your accountant’s bill because files transfer cleanly and require less conversion time. This saves hours of manual reconciliation — a smart tradeoff once you’re profitable.

Tier 4 – Enterprise or High Volume (Bench Accounting)

When you’re managing thousands of transactions a month, bookkeeping becomes a team job. That’s where Bench comes in — a dedicated, one-on-one accounting service built for large Shopify operations. Bench was even partnered with Shopify in the past to help merchants manage complex accounts. While these services are premium-priced, they bring unmatched accuracy and peace of mind for seven-figure stores.

Final Advice for Shopify Entrepreneurs

No matter where your business is, always choose the bookkeeping method that matches your stage. Keep it free and simple when you start, upgrade to Wave as you grow, and move to integrated accounting once you scale. Every upgrade should save you more time than it costs. And remember — your bookkeeping is part of optimizing your business, just like your store’s design or marketing.

For guided help setting up your Shopify store the right way, visit the 30-Day Beginner’s Shopify Program. You can also check out more resources and guides at ProfessorCommerce.com, or support future tutorials through Patreon.