Multiple shipping fees problem

Payments + Shipping & Fulfilment

Topic summary

Problem: A merchant wants Shopify to charge a single flat shipping fee even when an order spans multiple fulfillment locations. Customers are being charged multiple shipping fees despite items shipping in one parcel and a flat-rate policy regardless of order value or destination.

Current limitation: Shopify calculates shipping rates per location (each fulfillment origin), not per package. The platform cannot natively merge multiple location-based rates into one flat rate.

Suggested workarounds:

  • Fulfill from a single primary location to avoid location splits.
  • Use a third-party shipping app that supports rate merging at checkout.
  • Create custom shipping profiles to minimize how orders split across locations.

Status: No native solution; the issue is a known platform limitation. Practical solutions require operational changes or third‑party apps. Discussion remains open without a built-in fix from Shopify.

Summarized with AI on January 19. AI used: gpt-5.
1

Is it hopelessly and impossibly solvable to have Shopify manage shipping fees as one, even whit multiple shipping locations?? Some of our customers get charged for like 3 shipping fees, even though everything is shipped in the same parcel, and we always have a flat rate, dependless of order value or shipping location.

I’m going crazy here, please help!

4 Likes
4

This usually happens when shipping rates are being combined from different sources. Common causes are multiple shipping profiles, products assigned to different locations, or mixing carrier-calculated rates with manual rates.

I’d start by checking whether the products in the cart belong to different shipping profiles or ship-from locations, since Shopify will calculate shipping separately in those cases.

It’s also worth reviewing if any apps or carrier rates are adding their own fees on top. Once everything is aligned under the same profile and location, the multiple fees issue usually disappears.

8

No, it’s not impossible, but Shopify can’t do this natively.

By default, Shopify charges shipping per location, so if an order pulls inventory from 3 locations, customers get 3 shipping fees, even if you ship it in one box. To fix it, you must either:

Use one fulfillment location (or auto-split orders manually), or

Use an advanced shipping app that merges rates across locations, or

Move flat rate shipping to a shipping profile that ignores locations (limited and fragile).

So yes, it’s solvable, but not with out-of-the-box Shopify settings.