What is the best accounting software to use with Shopify?
QuickBooks Online and Xero are the two most common choices for Shopify stores. Both integrate with Shopify and handle what e-commerce businesses need. The software you pick matters less than how you connect it to Shopify and set it up for online selling.
Native Shopify integrations exist for both platforms, but they often create problems. Syncing every individual order generates thousands of transactions that slow down your books and make reconciliation nearly impossible. Most Shopify stores work better with a summarization tool like A2X or Synder that bundles daily sales into clean summary entries matching your Shopify payouts.
What your accounting software needs to handle for Shopify includes sales separated from shipping revenue, payment processing fees, refunds and chargebacks, sales tax collected as a liability, cost of goods sold, and gift card obligations. The payout timing issue trips up a lot of sellers. You sell $5,000 on Monday but Shopify pays you $4,800 on Thursday after deducting fees. If your books just show a $4,800 deposit, you’re missing true revenue and true costs.
QuickBooks Online tends to have more third-party app options and more accountants are familiar with it. Xero has a cleaner interface and some prefer how it handles bank reconciliation. For a typical e-commerce business, either works fine. Pick whichever your accountant prefers or whichever feels easier to navigate.
If you’re selling on multiple channels like Shopify plus Amazon plus Etsy, software choice matters even less. What matters is having a system that consolidates everything correctly. Multi-channel sellers often need help setting this up because the data flow gets complicated fast.
The real question isn’t which software is best. It’s whether your software gives you useful information about your Shopify business. Generic accounting setup doesn’t work for e-commerce. You need a chart of accounts structured for online selling, proper handling of the Shopify payout cycle, and reports that show true margins after all fees.
If you’re already using QuickBooks or Xero but your books are a mess of unreconciled transactions, the problem probably isn’t the software. It’s how Shopify data flows into it. A bookkeeper who understands e-commerce can clean this up and build a system that actually works going forward.
Utah's Trusted Bookkeeping Firm
First Step:
Start With a Call
Tell us what's going on and we'll let you know if we can help. We'll ask a few questions and give you a straightforward quote.
More Questions
What is a bookkeeper not allowed to do?
Bookkeepers cannot represent you before the IRS in audits, perform financial audits or attestation services, provide legal advice, or offer tax planning strategy. These services require CPAs, Enrolled Agents, or attorneys.
Read answerShould I Use QuickBooks Online for My Startup?
Yes, it works fine. QuickBooks Online handles what most startups need. The software isn't the hard part. Setup and consistency are.
Read answerWhat do most landscapers charge per hour?
Most landscapers charge $45 to $85 per hour as a billing rate. Basic lawn maintenance falls on the lower end while design work and hardscaping command higher rates. The right rate for your business depends on your actual costs.
Read answerCan ChatGPT create a cash flow statement?
ChatGPT can explain what a cash flow statement is and show you the format, but it can't create an accurate one from your actual business data. That requires access to your accounting records and the ability to verify the numbers.
Read answerHow much should I expect to pay a bookkeeper?
Most small businesses pay between $200 and $600 monthly for basic bookkeeping. Higher complexity or more comprehensive service typically runs $500 to $1,500. The actual cost depends on transaction volume, industry, and what's included.
Read answerHow Do I Calculate My Startup's Burn Rate?
Add up what you spend each month. That's your gross burn. Subtract any revenue and you get net burn. Divide your cash by net burn to find your runway.
Read answer