Why Does Splitting an Order in ShipStation Create Two Invoices?

Short answer: A split order is two shipments, and an accounting connector can treat each one as its own sale, so one order becomes two invoices. The better fix is not to use ShipStation as your source of truth for sales: pull sales from your store, such as Shopify, and use ShipStation’s connector for what it does best, which is the expense of your labels. Failing that, if all the boxes ship together to one address, use a multi-package shipment, which stays one shipment.

Why it happens

Split Ship divides one order into separate shipments, each with its own label and tracking number. That’s what it’s for. The order is still one sale, but anything that syncs ShipStation to your accounting may see two shipped records and create a record for each.

So the duplicate comes from how the two systems meet. ShipStation is reporting two shipments accurately, and the connector is deciding what to do with them.

Don’t pull sales from ShipStation

This is the fix I’d look at first. ShipStation knows what shipped. Your store knows what sold. Those are different records, and a split order is where the difference shows up.

Pull sales into your accounting from the source of truth, such as Shopify, so that one order stays one sale however many shipments it becomes. Then use the ShipStation connector for what only ShipStation knows, which is the cost of your labels.

How you set that up depends on your accounting tool and your connector, so check with them that sales aren’t being recorded twice before you turn anything off.

If the boxes ship together, use multi-package

Most orders that get split only because they need more than one box shouldn’t be split at all. A multi-package shipment is a single shipment in several boxes, under one master tracking number, so there’s only one shipment for a connector to pick up.

You can set which items go in which box, and the Recommend Package rule action can build the shipment at import. If your orders reach QuickBooks through ShipStation’s own connection, this is the route to take. ShipStation’s guidance there is not to split.

When you have to split

Multi-package only works when the boxes travel together. A split is the right tool when they can’t:

• Part of the order is on backorder. The items ship at different times, so they can’t be one shipment.
• Items ship from different warehouses. Each origin needs its own shipment.
• The order ships with USPS. USPS doesn’t support multi-package labels, so USPS volume uses separate shipments.

In these cases, two shipments are correct. If sales already come from your store, that’s the end of it. If they have to come through a ShipStation connector, the duplicate has to be fixed there. Connectors handle this differently, so I can’t tell you what yours does. Look in its settings or ask its support whether it invoices per shipment or per order, and whether a later shipment can update the existing invoice.

Splitting has other costs too. ShipStation documents that split orders stop syncing from the selling channel, and self-service Branded Returns stop working on them. That’s another reason to keep splits to the orders that need them.