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

Payments + Shipping & Fulfilment

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.
2

Hi Jason,

Unfortunately, there is no way around this when using multiple Shopify locations. When more than one location is called upon to satisfy an order, Shopify will charge per location and blend the rates.

The reasoning behind this process is that it is (in theory) costing you extra to ship because it is assumed you’re shipping the order from multiple locations. Of course, in reality, as is clear from your situation, that isn’t always the situation.

The only way to avoid this is to have all of your inventory in one location. Based on what you’ve described this might be possible, since the “house” locations are close by and only serve to warehouse excess inventory. However if you absolutely need to have inventory tracked in Shopify by location, there is unfortunately no workaround that I’m aware of.

Even if you use a third-party rate calculator like Intuitive Shipping, the issue would still exist. That’s because Shopify always splits the order into sub-carts for each location, sends the info to our system, we calculate the rate per sub-cart and send it back to Shopify, they blend each sub-cart calculation into a single combined rate at checkout.

Best regards,
Ron