Managing ecommerce accounting shouldn’t mean hours of CSV uploads and data cleanup. If you’re a Magento merchant looking to sync orders and customer invoices directly into QuickBooks Online with full line-item detail including taxes, shipping, and discounts, it’s completely doable with the right automation tool. Synder’s Magento QuickBooks integration makes it possible to automate your entire data flow, eliminating manual work and ensuring your books are always up to date.
Automate Magento order & invoice sync to QuickBooks Online
If you need to deal with returns, partial refunds, and credit memos in Magento, Synder detects and syncs them into QuickBooks Online with matching detail, keeping your revenue records clean.
Here’s how to replace your manual import process with a seamless Magento order sync to QuickBooks Online using Synder:
1. Connect Magento and QuickBooks Online to Synder
Sign up for a Synder account. Then, in the setup, connect both your QuickBooks Online account and Magento store. Synder supports direct integrations with both platforms, ensuring secure data transfer and eliminating third-party intermediaries.
2. Set up invoice sync
Synder imports invoices and credit memos from Magento as sales receipts. If your store accepts payments through Stripe or PayPal, be sure to connect those platforms separately as Magento alone won’t bring in fees or payouts. Just note: connecting Stripe or PayPal may create duplicate sales receipts, but it’s the only way to capture complete payment data, including fees and payouts, for accurate reconciliation. Synder’s support team is always here to help.
3. Map Magento data fields to QuickBooks
During setup, Synder helps you map fields like customer names, SKUs, payment methods, shipping, and taxes. You can also assign Magento payment gateways to QuickBooks clearing accounts. It ensures every synced Magento invoice import into QuickBooks aligns with your chart of accounts.
4. Enable line-item detail sync
Synder captures every order line item, including product names, SKUs, quantities, discounts, shipping costs, and sales tax, and matches them to QuickBooks items, so you get complete visibility into each transaction, without any data loss.
5. Automate the sync
Once your settings are in place, enable auto-sync. New Magento orders will flow into QuickBooks Online without any manual uploads. This automation reduces reconciliation errors and accelerates your month-end close.
Why Magento + QuickBooks integration with Synder just works
You know how dealing with CSV uploads can slow everything down and lead to mistakes. With automatic syncing, Magento orders go straight into QuickBooks: SKUs, taxes, shipping, discounts, all included. It keeps your reports accurate, your inventory aligned, and your records ready whenever you need them.
Join our Weekly Public Demo to see Synder in action—ask questions, get answers, and explore how it can work for your business.
FAQ
Can Magento orders be synced as invoices?
Indirectly. Synder imports Magento orders as sales receipts, not invoices. For more accurate tracking, especially of fees and payouts, make sure to connect your payment platforms like Stripe or PayPal as well.
Will line-item detail (tax, shipping, discounts) carry over into QuickBooks Online?
Yes. Synder imports full line-item detail from your Magento invoices, including product SKUs, quantities, taxes, discounts, and shipping fees, ensuring that your QuickBooks records reflect each transaction accurately.
Is historical import of Magento orders available?
Yes. If you need to catch up, Synder lets you back-sync past Magento orders into QuickBooks Online. On the Pro plan, the first 3 months of historical data import are included for free.
What happens if a Magento SKU doesn’t match a QuickBooks Online item?
Synder flags unmatched SKUs and allows you to create new items in QuickBooks or map them manually, ensuring clean data and inventory alignment.
Can Magento returns and credit memos sync automatically?
Yes. Synder supports syncing of returns, refunds, and credit memos, automatically recording them in QuickBooks with full detail.
