What doesn't sync from Shopify to ShipStation (and how to fix it)
The Shopify and ShipStation connection moves the important stuff well: orders, addresses, weights, customer notes, and tracking back to Shopify. But it has gaps, and you usually find them on a busy day, when a pick list is missing something or an order shows up that shouldn't have. Here's what doesn't come across, which of it is just a setting, and what to do about the rest.
This is based on ShipStation's own Shopify integration guide as of November 2026. Integrations change, so if something here doesn't match what you see, the guide wins.
1. Bin locations (and anything else in a product metafield)
This is the one I get asked about most. Shopify has no built-in bin location field, so most stores keep bins in a product metafield. ShipStation can map some Shopify data into custom fields, but product metafields aren't one of the options. So your bins never reach ShipStation, and its pick lists can't print or sort by them.
The fix: ShipStation prints and sorts by its own product field, Warehouse Location. Something has to copy the bin from Shopify into that field and keep it current. You can export and bulk-import it by hand for a small catalog that rarely moves, or set up a sync that does it automatically. I covered the options, ranked, in getting Shopify bin locations onto ShipStation pick lists, and the automatic version is what ShipStation bin sync does.
2. Order tags, order metafields and note attributes (off by default)
Tags like "gift wrap," "VIP" or "wholesale," fields a checkout app adds (a delivery date, a gift message), and Shopify's fraud risk assessment don't show up in ShipStation out of the box.
The fix: it's a setting. In ShipStation, open your Shopify store's settings and use Custom Field Mappings to map Order Tags, Order Metafields, Note Attributes or Fraud Risk to Custom Field 1, 2 or 3. Once they're there, you can filter on them and use them in automation rules, for example putting high-risk orders on hold. The catch: there are only three custom fields, so choose the ones your team actually acts on.
3. Automatic discounts
ShipStation's guide says Shopify's automatic discounts don't import. Discount codes do. If you print prices on packing slips or rely on ShipStation for customs values, an order with an automatic discount can look like it cost more than it did.
The fix: keep Shopify as your source for anything financial, and check customs values on international orders that used an automatic discount.
4. The currency the order was placed in
If you sell in multiple currencies, ShipStation can't retrieve the currency the customer actually paid in.
The fix: double-check declared values on international shipments, since that's where the wrong currency costs you.
5. Draft orders
Orders still in draft (phone orders, wholesale quotes, invoices waiting on payment) don't import.
The fix: complete the draft in Shopify. If an order is "missing" from ShipStation, check whether it's still a draft before anything else.
6. Older and closed orders
ShipStation only imports orders created in the last 90 days, and it skips closed and archived orders by default.
The fix: if you need to ship an older or archived order, turn on the Import Closed Orders setting for the store, or reopen the order in Shopify. If you mean to ship something that's more than 90 days old, plan on creating that shipment by hand.
7. Edits made after the order imports
Once an order is in ShipStation, edits in Shopify (a swapped size, an added item) only update automatically if the order is On Hold. Otherwise ShipStation may keep shipping the original version. ShipStation's guide mentions a "Use Fulfillable Quantity" setting that support has to enable for some edit cases.
The fix: put orders on hold while customers are still likely to change them, and if you edit orders often, ask ShipStation support about that setting.
8. Refunds that didn't cancel the order
This one is backwards: something syncs that shouldn't. An order refunded in Shopify can still import if its status didn't change, so it can end up shipped anyway.
The fix: cancel the order in Shopify, don't just refund it, whenever it shouldn't ship.
9. What goes back to Shopify
When you ship, ShipStation sends the fulfillment, tracking number, carrier and service back to Shopify. It doesn't send what the label cost you. HS codes also aren't saved to your ShipStation product defaults from Shopify.
The fix: use ShipStation's reports for shipping costs, and keep HS codes maintained wherever your customs forms read them.
The short version
- Just a setting: order tags, order metafields, note attributes, fraud risk, closed orders.
- A habit: complete drafts, cancel instead of only refunding, hold orders that might change.
- Be aware of it: automatic discounts, original currency, label costs, the 90-day window.
- Needs a sync: bin locations and other product metafields.
If bins are the gap that's slowing your pickers down, that's the one thing on this list a setting can't fix. Tell me how your setup looks and I'll tell you the fastest way to get bins on your pick lists, whether or not that's my sync.