Frequently asked questions

MyWorks lets you select your sync interval – every 5, 10, 30 or 60 minutes.

If you don’t want your data to sync in real-time, you can easily turn the sync on or off in your Settings. The real-time sync can also be adjusted by data type.

Use an integration tool like MyWorks to connect Shopify with QuickBooks. Install the MyWorks app from the Shopify app store and link your Shopify and QuickBooks accounts. Then, configure how and when you’d like your data to sync. Once setup is complete, all new sales data will sync automatically, saving you time and keeping your books accurate without manual entry.

When you sync Shopify with QuickBooks using MyWorks, orders, customers, products, taxes, shipping, and payments flow automatically between platforms. You have full control over what data is shared between platforms, how it is mapped and how often it syncs. Each Shopify order updates customer records and transaction data in QuickBooks, saving hours of manual entry. Inventory stays updated in real time, reducing errors and keeping your books accurate. MyWorks makes managing Shopify sales in QuickBooks reliable and straightforward.

It depends on your business model. Sales Receipts work best for retail/DTC orders paid at checkout — they keep your books and deposits in sync. Invoices are better for wholesale or B2B customers who pay later (Net 30, etc.), since they track outstanding balances. Daily Summaries consolidate all of a day’s sales into a single QuickBooks entry — ideal for high-volume DTC stores that don’t need order-by-order detail.

MyWorks also supports Hybrid Sync (available on Scale and Soar plans), which lets you mix transaction types using Shopify order tags — for example, syncing B2C orders as daily summaries while posting B2B orders individually as invoices. MyWorks is currently the only Shopify integration that supports all these sync modes within a single connection.

In MyWorks Sync, navigate to Settings → Payment Methods to map each Shopify payment method to the appropriate QuickBooks account. Shopify Payments should typically map to a clearing account, not a real bank account — this lets MyWorks record payouts as separate deposits to your actual bank account, so your QuickBooks data matches what you see in both Shopify and your bank statement.

One thing to note: newly created manual payment methods in Shopify (like cash or check) only appear in MyWorks mapping settings once at least one order has been paid using that method and synced. If you’ve just added a payment method and don’t see it yet, sync a test order through first.

MyWorks reads the tax data from each Shopify order and syncs it to QuickBooks based on your tax mapping settings (Sync → Map → Tax Rates). You can either map specific Shopify tax rates to QuickBooks tax codes, or enable “Sync tax as a separate line item” to record tax as its own line on the QuickBooks transaction — useful when QuickBooks tax codes don’t line up cleanly with your Shopify configuration.

Tax overrides are also supported, but rate names must match exactly (case-sensitive) for overrides to apply. For multi-jurisdictional setups — US multi-state sales tax, EU VAT, Canadian GST/PST, or international combinations — MyWorks handles tax line by line based on what Shopify recorded at checkout.

MyWorks syncs inventory in both directions — Shopify to QuickBooks, or QuickBooks to Shopify — depending on which platform you treat as your source of truth. You configure the direction, frequency, and which products are included under Sync → Settings → Inventory. The sync handles simple products, variations, and bundles.

One thing to know: Shopify rejects negative inventory quantities, so if QuickBooks has a product with a negative stock level, the sync to Shopify will fail with an INVALID_QUANTITY_NEGATIVE error until that’s corrected. Inventory changes don’t have to be triggered by sales either — manual stock adjustments in either platform sync the same way.

MyWorks syncs Shopify Payments payouts to QuickBooks as journal entries that move money from your Shopify Payments clearing account to your real bank account, net of Shopify Payments fees. This matches the actual flow of money — Shopify holds the funds, deducts fees, and then transfers the net payout to your bank.

To reconcile cleanly, ensure your QuickBooks bank account name exactly matches the one mapped in MyWorks (small differences like a “-1” suffix can cause the payout to post to the wrong account, which breaks bank-feed matching). Payouts in non-USD currencies and pending refunds can occasionally hold up automatic syncing — if a specific payout isn’t appearing, reach out to support with the payout ID.

MyWorks syncs refunds to QuickBooks when they’re processed in Shopify — refund sync is available on the Grow plan and above. Both full and partial refunds are supported, and they post as credit memos or refund receipts in QuickBooks depending on how the original order was synced (Sales Receipt vs Invoice).

One nuance: refunds that are in “pending” status in Shopify — which happens with some payment gateways like Shop Pay or PayPal — only sync once they finalize. If you’ve issued a refund and it hasn’t synced after a few hours, check the refund status in Shopify before troubleshooting further.

QuickBooks requires product names to be unique — specifically, the first 50 characters must be unique. If two Shopify products share the same first 50 characters, the second one will create a duplicate or trigger QuickBooks error 6240 instead of syncing cleanly.

Two ways to fix this: (1) Map existing QuickBooks products to your Shopify products in Sync → Map → Products before pushing — that way the sync updates the existing item rather than creating a new one; (2) Rename Shopify products so the first 50 characters are unique, then push again. The same rule applies to variations — they sync against the variant name and SKU.

The QuickBooks Web Connector is the local component that moves data between MyWorks and QuickBooks Desktop. Most Web Connector issues come down to one of three things:

1. QuickBooks Desktop is running as a different Windows user than the Web Connector — make sure both run as the same user with admin permissions.
2. Multiple QuickBooks instances are open — close all of them, then reopen QuickBooks once.
3. The .QWC connection file is outdated after a QuickBooks company file rename or move — download a fresh .QWC from your MyWorks Sync dashboard and re-add it.

For QBWC 1039 errors specifically, the most common fix is closing QuickBooks fully and reopening it to clear orphaned processes. If the queue isn’t clearing or you’re seeing timeout errors, open a support thread with your license key so the team can investigate.

Shopify doesn’t fully support multi-level assemblies or bundled products natively like QuickBooks Desktop does, although there’s quite a few apps that make this possible in Shopify. Once a bundle has been created in Shopify; apps like MyWorks can help keep inventory levels in sync between QuickBooks and Shopify, but complex assemblies may require additional setup or inventory management tools. Always check that your products and stock levels map correctly to avoid overselling or errors.

In QuickBooks, Shopify fees (like transaction or processing fees) are normally recorded as expenses inside an expense account, named “Shopify Fees” or “Merchant Fees.” This will then correctly show as its own expense line on a Profit and Loss statement. When setting up a sync with QuickBooks, ensure your integration correctly maps these fees when handling Shopify payouts. This keeps your income accurate, accounts for expenses properly, and helps you track your net sales and profit.