Frequently Asked Questions
Common questions about QuickBooks-Shopify integration, answered clearly.
Is daily batching better than per-order posting?
Batching speeds reconciliation and keeps QuickBooks lean. Per-order is fine at low volume or when you need granular reporting.
How do I post gateway fees correctly?
Record gross sales, then fees as expenses against the payout; accounting-grade tools automate this per gateway.
Can I do this with Zapier?
Yes for simple cases, but watch taxes, refunds, and inventory—connectors don't enforce accounting logic.
What's the difference between QuickBooks Online and Desktop for Shopify integration?
QBO offers real-time cloud-based integration with OAuth. Desktop requires Web Connector and sync windows. Most modern apps prefer QBO for easier setup.
Do I need an accounting-grade app if I'm under 100 orders/month?
Not necessarily. Manual CSV or simple connectors can work at low volume. Consider an app when you need accurate COGS, multi-location inventory, or spend more than an hour/week on manual posting.
How do refunds work in QuickBooks?
Full refunds create credit memos. Partial refunds require line-item credits. Gateway fees are partially refunded (you lose the fixed 30¢). Apps handle this complexity automatically.
Can I sync inventory between Shopify and QuickBooks?
Yes, but only with accounting-grade apps. Manual CSV and connectors don't reliably sync inventory quantities, especially across multiple locations.
What if I sell on Amazon, eBay, and Shopify?
Use a multichannel accounting app like Webgility. It connects all platforms, consolidates posting to QuickBooks, and tracks profitability per channel.
How long does integration setup take?
Manual CSV: ongoing work. Zapier: 30-60 minutes initial setup. Accounting-grade apps: 1 hour setup, then automated daily. Choose based on your ongoing time vs upfront time preference.
What's the ROI of using an integration app vs manual methods?
At 200 orders/day and 5 min per manual entry, you save ~80 hours/month. At $30/hour labor cost, that's $2,400 saved vs $99-199 app cost. ROI is immediate for most businesses over 100 orders/month.
Still have questions?
We're here to help. Email us at hello@quickbookstoshopify.com with your specific integration questions.