Shopify and BigCommerce help businesses build online stores, manage products, process orders, and sell across multiple markets. However, as order volumes and product catalogs grow, ecommerce businesses often face challenges with inventory accuracy, order synchronization, warehouse operations, shipping, and returns.
Shopify and BigCommerce manage the customer-facing ecommerce experience, but growing businesses may need additional tools to control what happens after an order is placed.
A 3PL warehouse management system connects ecommerce orders with warehouse operations. Fulfillor is a cloud-based WMS designed to support inventory management, order fulfillment, shipping workflows, and multi-client warehouse operations.
This guide explores seven common Shopify and BigCommerce fulfillment challenges and explains how a WMS can help improve inventory visibility, order accuracy, and warehouse efficiency.
How Shopify and BigCommerce Fit into the Fulfillment Process
Shopify: Flexible Ecommerce Platform for Growing Stores
Shopify is a cloud-based ecommerce platform that helps businesses create online stores, manage products, process payments, and connect with sales and marketing applications.
Its user-friendly interface and large integration ecosystem make it suitable for businesses at different stages of growth. However, as Shopify order fulfillment becomes more complex, businesses may need a dedicated system to manage warehouse inventory, picking, packing, shipping, and returns.
Its user-friendly interface and broad Shopify integration ecosystem make it suitable for businesses at different stages of growth.
BigCommerce: Built-In Commerce Features for Multichannel Selling
BigCommerce is a cloud-based ecommerce platform that supports online storefronts, product management, payments, SEO features, and multichannel selling.
It provides strong tools for managing ecommerce operations, but growing businesses may still need warehouse management software to coordinate BigCommerce order fulfillment, inventory updates, shipping workflows, and stock across multiple locations or channels.
Businesses can connect the platform with a BigCommerce integration to coordinate ecommerce orders with warehouse workflows.
Both platforms manage the online shopping experience. A WMS supports the warehouse activities that take place after an order is placed.
Shopify, BigCommerce, and WMS Responsibilities
The table below shows where ecommerce platform functions end and warehouse management responsibilities begin.
| Fulfillment Area | Shopify and BigCommerce Role | Warehouse Management System Role |
|---|---|---|
| Order Capture | Receive customer orders and store order details. | Import orders and route them into warehouse fulfillment workflows. |
| Inventory Visibility | Display available product quantities to online customers. | Track physical inventory by SKU, bin, warehouse, status, or client. |
| Order Allocation | Record the products and quantities purchased by the customer. | Allocate available stock and assign the order to the appropriate warehouse. |
| Picking and Packing | Provide basic order information after a purchase is completed. | Guide warehouse workers through barcode scanning, picking, packing, and verification. |
| Shipping | Show shipping options and customer delivery information. | Create shipping labels, record tracking details, and confirm dispatch. |
| Returns | Capture customer return requests and order information. | Receive, inspect, classify, restock, or quarantine returned products. |
| Multi-Store Management | Manage products and orders across ecommerce storefronts. | Centralize inventory and fulfillment across stores, clients, channels, and warehouses. |
7 Shopify and BigCommerce Fulfillment Challenges a WMS Can Solve
Once orders begin moving into the warehouse, fulfillment teams need accurate inventory, reliable order data, structured picking and packing, shipping coordination, and returns control.
These processes become harder when a business operates multiple stores, warehouses, sales channels, or client accounts.
Here are seven common fulfillment challenges and how a warehouse management system can help address them.
1. Disconnected Systems and Inconsistent Data
Shopify and BigCommerce stores often connect with marketplaces, shipping carriers, accounting tools, and warehouse systems. When these integrations do not exchange data consistently, teams may need to enter information manually or correct incomplete records.
Common problems include:
- Missing or duplicate orders
- Incorrect product information
- Delayed inventory updates
- Inconsistent order statuses
- Manual data entry between systems
Centralizing Ecommerce and Warehouse Data
Centralized integrations bring order, inventory, fulfillment, and shipment data from connected ecommerce channels into one operational view.
Rather than managing every application separately, teams can use structured workflows to move orders from import through picking, packing, and shipping.
2. Delayed Order Synchronization
Orders placed through Shopify or BigCommerce must reach the warehouse quickly. Delayed imports can cause orders to miss same-day shipping cutoffs or remain unprocessed until someone notices them.
This becomes especially difficult when a company operates several online stores or manages orders for multiple fulfillment clients.
Moving Orders Into Fulfillment Faster
New ecommerce orders can flow directly into a shared warehouse queue, where teams can allocate inventory, prioritize urgent shipments, and begin fulfillment. Warehouse teams can view new orders, prioritize urgent shipments, allocate stock, and begin fulfillment without relying on spreadsheets or manual downloads.
This creates a more consistent Shopify order fulfillment and BigCommerce order fulfillment process.
3. Inventory Management Complexity
Inventory management becomes more difficult as product catalogs, order volumes, and warehouse locations increase.
Inventory records may become inaccurate because of:
- Delayed stock updates
- Unprocessed returns
- Damaged inventory
- Manual adjustments
- Orders placed through multiple channels
- Stock stored in different warehouses
These discrepancies can lead to overselling, stockouts, delayed orders, and unnecessary replenishment.
Tracking Inventory as Stock Moves
Recording every receipt, movement, pick, pack, return, and adjustment creates a more reliable picture of available stock.
Warehouse teams can view stock by SKU, location, status, warehouse, or client. When inventory data is synchronized with ecommerce stores, Shopify and BigCommerce can display more reliable stock availability.
4. Fragmented Multichannel Inventory
Many ecommerce businesses sell through more than one channel. A company may operate a Shopify store, a BigCommerce site, marketplaces, wholesale accounts, and physical retail locations.
Without centralized multichannel inventory management, each channel may show a different stock quantity.
Creating One Inventory Record Across Channels
One shared inventory record helps connected stores, marketplaces, and warehouse locations work from the same stock position.
This helps businesses:
- Reduce conflicting stock quantities
- Track inventory across multiple warehouses
- Reserve products for specific channels
- Improve inventory reconciliation
- Reduce manual stock adjustments
For 3PL providers, centralized inventory control also helps separate stock by client while managing it through one warehouse platform.
5. Picking and Packing Errors
Ecommerce platforms send orders to the warehouse, but they do not always control how workers physically pick and pack products.
Paper lists and manual product checks can result in:
- Incorrect SKUs
- Wrong quantities
- Missing items
- Incomplete orders
- Products packed for the wrong customer
These mistakes increase returns, replacement costs, and customer service work.
Using Barcode Validation to Prevent Fulfillment Errors
Barcode-based workflows guide workers through product, quantity, location, and packing checks before an order reaches dispatch.
Product scans, quantity checks, packing verification, and exception alerts help teams identify mistakes before an order is shipped.
This improves order accuracy without requiring workers to rely entirely on memory or handwritten instructions.
6. Shipping and Tracking Complexity
Businesses may use different carriers and shipping services depending on destination, package size, delivery speed, or customer preference.
Selecting services manually and copying tracking numbers back into Shopify or BigCommerce takes time and increases the risk of errors.
Connecting Shipping Labels, Tracking, and Dispatch
Connecting order fulfillment with carrier workflows allows teams to create labels, record tracking details, confirm dispatch, and return shipment updates without repeated data entry. Warehouse teams can create labels, record tracking details, confirm dispatch, and update shipment statuses from the same system used to manage the order.
This reduces duplicate entry and gives merchants better visibility into shipped orders.
7. Scaling Fulfillment Operations
A fulfillment process that works for one store may become difficult to manage when a business adds more products, warehouses, sales channels, or clients. For businesses working with a Shopify 3PL or BigCommerce 3PL, standardized workflows make it easier to manage inventory and orders across clients, stores, and warehouse locations.
Growth can expose problems such as:
- Inconsistent warehouse procedures
- Limited inventory visibility
- Slower order processing
- More picking errors
- Increased manual reporting
- Difficulty onboarding new clients or stores
Standardizing Workflows as Fulfillment Grows
Standardized receiving, picking, packing, shipping, and returns workflows make it easier to add stores, clients, and warehouse locations without creating a separate process for each one.
Fulfillor supports ecommerce and multi-client warehouse operations by connecting store orders with warehouse execution. This allows businesses and 3PL providers to manage additional order volume without creating a separate manual process for every store or client.
Conclusion
Shopify and BigCommerce manage online storefronts, products, customer orders, and transactions. As fulfillment operations grow, businesses may need a dedicated system to manage physical inventory, warehouse tasks, shipping, and returns.
A WMS becomes especially useful when a business operates multiple stores, warehouses, sales channels, or client accounts. It helps connect ecommerce orders with warehouse execution while reducing manual updates, inventory discrepancies, and inconsistent fulfillment processes.
Fulfillor supports Shopify, BigCommerce, and multi-client fulfillment workflows through centralized inventory, order processing, picking, packing, shipping, and returns management.
Book a demo to evaluate whether Fulfillor fits your ecommerce or 3PL fulfillment operation.