Shopify and BigCommerce help businesses build online stores, manage products, process customer orders, and sell across multiple markets. As order volumes and product catalogs grow, however, fulfillment becomes more complicated once those orders reach the warehouse.
A 3PL warehouse management system connects ecommerce order data with warehouse operations. For businesses and 3PL providers managing Shopify or BigCommerce fulfillment, this can help coordinate inventory, order processing, warehouse execution, shipping, and returns.
This guide covers seven common Shopify and BigCommerce fulfillment challenges and explains where a WMS can provide additional warehouse-level control.
Where a WMS Adds Control Beyond Shopify and BigCommerce
Shopify and BigCommerce can manage ecommerce orders, inventory availability, fulfillment locations, and customer-facing order information. A WMS adds deeper warehouse execution controls for inventory status, picking and packing, barcode validation, multi-client operations, shipping workflows, returns, and other processes tied to physical warehouse activity.
| Area | Ecommerce Platform Role | Where WMS Adds Control |
|---|---|---|
| Orders | Captures orders and maintains ecommerce order information | Connects orders to warehouse execution, client rules, queues and operational workflows |
| Inventory | Can maintain product availability and location-level inventory information | Tracks physical inventory by bin, status, allocation, client and warehouse activity |
| Fulfillment | Supports fulfillment locations and ecommerce fulfillment logic | Controls picking, barcode validation, packing and warehouse exceptions |
| Shipping | Maintains delivery and shipment information | Coordinates labels, carrier workflows, dispatch confirmation and tracking |
| Returns | Maintains order and customer information | Controls receiving, inspection, quarantine, restocking and disposition |
7 Shopify and BigCommerce Fulfillment Challenges a WMS Can Solve
1. Ecommerce and Warehouse Data Fall Out of Sync
Problems appear when ecommerce and warehouse systems do not exchange information consistently or when orders take too long to reach the warehouse.
Common issues include:
- Missing, delayed, or duplicate orders
- Incorrect product or inventory information
- Inconsistent fulfillment and order statuses
- Repeated manual data entry
For a single low-volume store, some of this may still be manageable manually. The problem becomes much more noticeable when several ecommerce stores or 3PL clients depend on the same fulfillment operation. The risk grows when multiple stores or 3PL clients depend on the same fulfillment operation.
This reduces dependence on spreadsheets and CSV downloads while helping warehouse teams process Shopify and BigCommerce orders through a consistent fulfillment workflow.
2. Ecommerce Routing Does Not Cover Every Warehouse Rule
Ecommerce platforms can route orders to fulfillment locations, but warehouse execution may require additional rules tied to usable inventory, client ownership, service levels, warehouse capacity, cutoff times, picking workload, or carrier requirements.
The correct location may depend on:
- Usable inventory availability
- Client ownership
- Warehouse capacity or workload
- Shipping destination
- SLA or service requirements
- Fulfillment rules and cutoff times
Without a consistent routing process, an order may be assigned to a location that does not have usable stock or cannot meet the required shipping window.
A WMS can apply warehouse-level inventory and fulfillment rules when assigning orders to a location or workflow.
3. Sellable Inventory Does Not Always Match Warehouse Inventory
A Shopify or BigCommerce store can only display useful inventory availability when the warehouse records behind it are accurate. Differences can result from receiving or putaway errors, missed inventory movements, damaged or quarantined stock, unprocessed returns, picking discrepancies, or manual adjustments.
Physical stock may exist in the warehouse without being sellable because it is already allocated, picked, damaged, quarantined, returned, or awaiting inspection.
A WMS records inventory as products move through receiving, storage, picking, packing, transfers, adjustments, and returns.
Using inventory management, warehouse teams can view stock by SKU, warehouse, bin, status, or client.
4. Shared Inventory Creates Allocation Conflicts Across Stores and Channels
A company might operate a Shopify store, a BigCommerce site, marketplaces, wholesale accounts, or physical retail locations while drawing stock from the same warehouse network.
The challenge is not simply knowing how much inventory exists. It is determining what inventory remains available after orders from different channels begin competing for the same stock.
This can help businesses:
- Track inventory across warehouses
- Account for inventory already allocated or reserved against orders
- Reduce conflicting stock availability across connected stores
For a 3PL, the same principle applies across client accounts. Inventory can remain separated by ownership while warehouse teams manage fulfillment through the same operational system.
5. Shopify and BigCommerce Orders Still Need Accurate Picking and Packing
Receiving an order from Shopify or BigCommerce does not guarantee that the warehouse will pick the correct SKU, quantity, or package.
Manual picking and packing can lead to incorrect SKUs, quantities, missing items, or products assigned to the wrong order. These errors can result in replacement shipments, returns, additional shipping costs, and customer service work.
Barcode-based workflows can validate products, quantities, storage locations, and packing steps before an order leaves the warehouse.
Workers can scan products while picking and packing, allowing the WMS to check those scans against the ecommerce order.
6. Shipping Updates Must Return to Shopify or BigCommerce
The warehouse must still create the shipment, generate the label, capture tracking information, and confirm that the order has been dispatched.
When those steps are handled separately, teams may end up copying tracking numbers or shipment statuses between systems.
Connecting ecommerce orders with shipping management workflows allows warehouse teams to generate labels, capture tracking details, and confirm dispatch through the fulfillment process.
Shipment information can then be returned to Shopify or BigCommerce without repeatedly entering the same details.
7. Returned Products Need a Warehouse Decision Before Restocking
A Shopify or BigCommerce return does not automatically mean the product should immediately become available for sale again.
When a returned item reaches the warehouse, teams may need to:
- Identify the original order
- Inspect the product and record its condition
- Decide whether it can be restocked
- Place damaged or questionable inventory on hold
If this process is not controlled, a storefront may show returned inventory as available before the warehouse has confirmed that the item can actually be sold again.
A structured returns management workflow can connect returned inventory with warehouse receiving and inspection.
Only after that decision should the warehouse inventory status determine whether the item becomes available to Shopify or BigCommerce again.
When Does Shopify or BigCommerce Fulfillment Need a WMS?
Not every Shopify or BigCommerce business needs warehouse management software.
Common signs include:
- Inventory is managed across multiple warehouses or fulfillment locations.
- Several stores or channels depend on shared warehouse inventory.
- Picking and packing require barcode-based verification.
- Warehouse teams rely heavily on spreadsheets or manual imports to connect ecommerce and warehouse operations.
- A 3PL manages separate inventory, orders, and fulfillment rules for multiple ecommerce clients.
At that stage, the decision is not whether Shopify or BigCommerce should be replaced. The question is whether the ecommerce platform needs to be connected with a system built specifically for warehouse execution.
Shopify and BigCommerce Fulfillment With Fulfillor
Fulfillor connects Shopify and BigCommerce with warehouse execution while keeping ecommerce and fulfillment data synchronized. The Shopify WMS integration can support order edits, cancellations, inventory updates, controlled order release, and tracking synchronization, while the BigCommerce WMS integration supports SKU and inventory-location mapping, multi-storefront workflows, controlled order imports, and fulfillment updates.