How can I prevent double shipping charges on multi-location orders in Shopify?

Topic summary

A Shopify merchant discovered customers were being charged double shipping fees (£7.98 instead of £3.99) when orders pulled inventory from multiple locations. The store uses three locations—a main shop and two nearby home warehouses for overflow stock—but ships all items together in one package.

Core Issue:

  • Shopify automatically splits orders by location and charges shipping per location, even when items ship together
  • This behavior is built into Shopify’s system and affects third-party shipping calculators as well

Proposed Workarounds:

  • Set shipping as free for warehouse locations and only stock high-value items (above free shipping threshold) there
  • Use apps like ShipMagic or Bespoke Shipping, which claim to solve this for flat-rate shipping scenarios
  • Consolidate all inventory into one Shopify location (eliminates multi-location tracking)

Current Status:
The discussion remains unresolved as an ongoing Shopify limitation. Multiple merchants report the same frustration, citing lost sales and customer complaints. One merchant claims Shopify support promised reimbursement for offering free shipping as a temporary fix, but never followed through. App-based solutions exist but require setup complexity and may need specific Shopify plan levels.

Summarized with AI on October 30. AI used: claude-sonnet-4-5-20250929.

Was just thinking Ron would it be possible for me to set shipping as free for Jason and Dave Warehouse (as you can do a different rate for each location I believe?) and then only stock more expensive products (complete skateboards) which would go over our free shipping policy anyway? As long as I don’t have any small priced products available at those locations (as need to ensure I don’t ship them for free) then I wouldn’t mind the shipping being free.