What Is a WMS (Warehouse Management System) and How to Connect It to Your Online Store
A WMS (Warehouse Management System) is software for running a warehouse. Unlike basic stock records, it doesn't just tell you how much of something you have, but also exactly where it sits, who should pick it, in what order and into which parcel. A warehouse with a WMS works with barcode scanners, and every movement of goods is recorded the moment it happens. For an online store, that means fewer order errors, faster shipping and stock levels on the website that match reality.
In this article we explain what a WMS does, how it differs from the inventory module in accounting software or an ERP, when an online store needs one, how to connect it to Shopify and when it's better to hand your warehouse to a fulfillment company instead of running your own WMS. At the end you'll find an overview of WMS solutions used in the Czech Republic and worldwide.
Key takeaways
- A WMS manages warehouse processes: receiving, putaway, picking, packing, shipping, stocktaking and returns.
- Compared with the stock records in accounting software, it knows the exact location of goods and guides warehouse staff step by step.
- An online store typically needs a WMS when shipping errors and manually searching for goods start costing customers and time.
- The alternative to your own warehouse with a WMS is fulfillment: a specialized company takes over both storage and shipping.
Table of contents
- What WMS stands for
- What a WMS does in the warehouse
- WMS, ERP and stock records: what's the difference
- When an online store needs a WMS
- How a WMS speeds up picking
- Barcodes, scanners and other equipment
- How to connect a WMS to Shopify
- Your own warehouse with a WMS, or fulfillment?
- Overview of WMS solutions in the Czech Republic and worldwide
- How much a WMS costs
- Implementing a WMS step by step
- Frequently asked questions (FAQ)
What WMS stands for
WMS stands for Warehouse Management System. It's software that controls the physical movement of goods in a warehouse: from the moment they arrive from the supplier, through storage on a shelf, to shipping to the customer. The key word is "controls". A WMS doesn't just record what happened; it tells warehouse staff what to do: where to put goods away, where to pick them from and which route to take through the warehouse.
In larger companies, a WMS is a standalone system that works alongside the ERP. Smaller companies and online stores often use a WMS as a cloud service connected to the store and accounting software. Some ERPs offer a WMS as an add-on module.
What a WMS does in the warehouse
A WMS covers every process goods go through in the warehouse. Each step is confirmed by scanning a barcode, so the system knows exactly what happened where and who did it.
| Process | What the WMS does | What you gain |
|---|---|---|
| Receiving | Checks the delivery against the purchase order, records batches and expiry dates | You spot discrepancies in deliveries immediately, not at stocktaking |
| Putaway | Suggests a free shelf location based on the size and turnover of the goods | Fast-moving goods close to shipping, no searching |
| Storage locations | Records the exact location of every item (rack, shelf, position) | Even a new temp worker can find the goods |
| Picking | Creates a pick list and the optimal route through the warehouse | Less walking, fewer errors |
| Packing and shipping | Checks parcel contents, prints the carrier label, passes on the tracking number | The parcel contains exactly what the customer ordered |
| Stocktaking | Continuous cycle counts by location without stopping operations | The warehouse doesn't have to close for stocktaking |
| Returns | Receives returned goods, checks their condition, returns them to stock | Returned goods are quickly back on sale |
| Reports | Staff performance, turnover, slow movers, error rates | You know where the warehouse loses time and money |
WMS, ERP and stock records: what's the difference
Stock records know how much you have, the ERP knows what it's worth and who owns it, and the WMS knows exactly where it sits and how to get it to the customer. All three deal with the warehouse, but from different angles.
| Stock records (online store, accounting software) | ERP inventory module | WMS | |
|---|---|---|---|
| Quantity in stock | Yes | Yes | Yes |
| Inventory valuation and accounting | Partly | Yes | No, passes it to the ERP |
| Exact shelf location | No | Sometimes, basic | Yes |
| Directing warehouse staff | No | Limited | Yes |
| Scanners and mobile terminals | No | Sometimes | Yes |
| Route and picking optimization | No | No | Yes |
In practice, a WMS complements an ERP or accounting software. The ERP handles finance, purchasing and invoicing, the WMS handles the physical work in the warehouse and the online store handles sales. What an ERP involves and which systems are used in the Czech Republic is explained in our article What Is an ERP System.
When an online store needs a WMS
An online store needs a WMS when the warehouse can no longer run on the memory of experienced staff. There is no exact threshold in number of orders; it depends on the size of your product range and warehouse. Typical signs:
- customers receive the wrong item, the wrong size or incomplete parcels,
- staff search for goods because only one person knows where they are,
- stock levels in the online store don't match and you sell what you don't have,
- training a new person in the warehouse takes weeks,
- shipping can't keep up before Christmas and during promotions,
- stocktaking means closing the warehouse for a day or two,
- you carry goods with batches or expiry dates (cosmetics, food, supplements) and need to make sure the right ones go out first.
A small online store with a few dozen products in one room doesn't need a WMS. Inventory tracking in Shopify or in accounting software is enough. Once your range runs into hundreds or thousands of items and you ship dozens to hundreds of orders a day, a WMS usually pays for itself in time saved and errors avoided.
How a WMS speeds up picking
Picking is the most expensive part of warehouse work, because staff spend most of their time walking. A WMS shortens walking and reduces errors in several ways:
- Order picking: one order, one trip. Simple, suitable for smaller warehouses.
- Batch picking: a picker collects several orders at once into the compartments of a cart. For an online store with small orders, it saves a lot of walking.
- Zone picking: each picker has their own zone of the warehouse and orders are consolidated at the end.
- Wave picking: orders are released in waves based on carrier pickup times.
- Optimal route: the WMS sorts items so the picker walks through the warehouse in one direction without doubling back.
- Random (chaotic) storage: goods are put away in the first suitable free location rather than a fixed position. Impossible without a WMS, a space saver with one.
- FIFO and FEFO: the WMS ensures that goods that arrived first (FIFO) or expire first (FEFO) go out first.
Barcodes, scanners and other equipment
A WMS only works with labeled goods and locations. Every product needs a barcode and every shelf location its own label. Basic equipment:
- Barcodes on products: EAN codes from the manufacturer, or your own internal codes printed in the warehouse.
- Labels on racks and positions.
- Mobile terminals or scanners: staff see their tasks and confirm each step. For smaller warehouses, a rugged phone with an app is often enough.
- Label printers for shipping labels and internal codes.
- A scale at the packing station to check parcel weight and the correct shipping price.
It pays to invest in equipment before launching the WMS, not during the rollout. Unlabeled goods are the most common reason WMS implementations stall.
How to connect a WMS to Shopify
The WMS and Shopify must automatically exchange orders, stock levels and tracking numbers. Without an integration, orders would be retyped by hand and the whole benefit of the WMS would be lost. The data flow looks like this:
| Data | Direction | Why |
|---|---|---|
| New orders | Shopify → WMS | The warehouse starts picking right after payment |
| Stock levels | WMS → Shopify | Customers see real availability, no overselling |
| Tracking number and shipment | WMS → Shopify | The customer receives an email with shipment tracking |
| Cancellations and order changes | Shopify → WMS | The warehouse doesn't pick a canceled order |
| Returns | WMS → Shopify | Returned goods go back on sale and the refund is triggered |
| Products and barcodes | Shopify or ERP → WMS | A new product is entered once |
What to watch out for:
- One source of truth for stock. When the WMS runs the warehouse, stock levels must not be changed manually in Shopify. Otherwise the systems drift apart.
- Stock sync frequency. The more often, the lower the risk of overselling, especially at peak times.
- Multiple locations. Shopify can work with multiple warehouses (locations). If you have your own warehouse plus a store or an external warehouse, set which location fulfills orders.
- Carriers. Labels are usually printed by the WMS. If you use Balíkobot (a Czech multi-carrier shipping service), check where it connects; see our article Balíkobot Integration with Shopify.
- Accounting. Stock movements and invoices must also reach your accounting system or ERP. The integration is described in our article Accounting on Shopify.
Some WMS solutions have a ready-made Shopify integration; elsewhere the connection is built via the API. We can set up your WMS integration with Shopify as part of our Shopify customizations and integrations.
Your own warehouse with a WMS, or fulfillment?
Instead of running your own warehouse and WMS, you can hand storage and shipping over to a fulfillment company. It stores, picks, packs and ships goods to your customers, with its own WMS included in the price. The decision depends on volume, product range and how much control you want over shipping.
| Own warehouse with a WMS | Fulfillment | |
|---|---|---|
| Control over packing and quality | Full | Depends on the contract and the warehouse's capabilities |
| Costs | Fixed (premises, staff, software) | Variable (per item, per order, storage) |
| Seasonal peaks | You have to handle them yourself | Handled by the fulfillment provider's capacity |
| Shipping rates | Your own carrier contracts | Often better thanks to the warehouse's volume |
| Best for | Custom packaging, manufacturing, in-store pickup, your own team | Growing online stores that don't want to deal with a warehouse |
Fulfillment pays off mainly for growing online stores that don't want to build a warehouse and a team. Your own warehouse with a WMS makes sense when packaging is part of your brand, your products are specific (bulky, fragile or customized goods), or you already have a warehouse and staff.
Overview of WMS solutions in the Czech Republic and worldwide
Globally, large-scale WMS solutions for big distribution centers lead the market, while Czech online stores often choose cloud WMS built specifically for e-commerce, or the inventory module of their ERP.
Worldwide: systems for large distribution centers
In its 2025 WMS evaluation, the analyst firm Gartner names Manhattan Associates, Blue Yonder, Infios, SAP and Oracle among the market leaders. These are systems for large warehouses with automation, robots and thousands of orders an hour. Implementing them takes months and costs millions of crowns, which is far too much for a typical Czech online store.
In the Czech Republic: WMS for online stores and ERP modules
There is no public ranking of WMS market shares in the Czech Republic. An overview of the types of solutions a Czech online store encounters most often:
| Solution | Type | Who it's for |
|---|---|---|
| Depoto | Cloud WMS for online stores | Stores on Shoptet, Upgates, Shopify, WooCommerce and other platforms |
| Elasticr WMS | Cloud WMS | Online stores, B2B companies and manufacturers, API integration |
| Skladon | Fulfillment with its own WMS | Online stores that want to outsource their warehouse |
| ERP inventory modules (Helios, K2, ABRA, Money) | Part of the ERP | Companies already using that ERP |
| SAP EWM, Oracle WMS, Manhattan | Enterprise WMS | Large distribution centers and multinationals |
| Custom WMS | Custom development | Warehouses with specific processes |
The difference from the global market is mainly size: the Czech market consists of smaller warehouses, where what matters is speed of implementation, integration with Czech e-commerce platforms and carriers, and a price in the thousands of crowns a month rather than multimillion projects.
How much a WMS costs
Cloud WMS for online stores is paid monthly, usually based on the number of orders, users or warehouses. Enterprise WMS is paid through a license and costly implementation. Your budget should include:
- Subscription or license for the WMS.
- Implementation and integration with the online store, ERP and carriers.
- Hardware: scanners or terminals, label printers, shelf labels.
- Relabeling the warehouse: labeling locations and products without barcodes.
- Training for warehouse staff.
Calculate the return from time saved by staff, fewer shipping errors (each error means return shipping, a new parcel and an unhappy customer) and less unsellable stock.
Implementing a WMS step by step
- Describe your current warehouse processes: receiving, putaway, picking, packing, returns. You'll find out where you lose time.
- Design the warehouse layout and a location labeling system. Fast-moving goods belong close to shipping.
- Choose a WMS based on its integration with your platform, carriers and accounting.
- Label goods and locations with barcodes.
- Do an initial stocktake directly into the WMS. Starting with inaccurate stock makes no sense.
- Connect Shopify, carriers and accounting and test the entire flow with test orders.
- Train your staff and go live outside the season, ideally in a quiet month, not before Christmas.
- After a month, review the error and performance reports and adjust the warehouse layout.
The most common mistakes: going live in peak season, unlabeled goods, an inaccurate initial stocktake and manual changes to stock outside the WMS. Why you shouldn't change systems right before Black Friday is explained in our technical checklist for Black Friday and Christmas.
Frequently asked questions (FAQ)
What is a WMS?
A WMS (Warehouse Management System) is software for running a warehouse. It records the exact location of goods, manages receiving, putaway, picking, packing and shipping, and confirms every step with a barcode scan. Unlike basic stock records, it doesn't just record what happened but tells warehouse staff what to do.
What is the difference between a WMS and an ERP?
An ERP runs the whole company, including finance, purchasing, invoicing and inventory valuation. A WMS runs the physical work in the warehouse: where goods are, who picks them and how they're packed. The systems complement each other. The WMS sends stock movements to the ERP, and the ERP sends orders and products to the WMS.
Does a small online store need a WMS?
Usually not. An online store with a few dozen products in one room can get by with inventory tracking in Shopify or in accounting software. A WMS pays off when the product range grows into hundreds or thousands of items, dozens to hundreds of orders ship every day and shipping errors start costing customers.
How do you connect a WMS to Shopify?
Through a ready-made WMS integration for Shopify or via the API. Shopify sends new orders and cancellations to the WMS, and the WMS returns stock levels, tracking numbers and return information. It's important that only one system changes stock levels, otherwise the data drifts apart.
Which is better, your own warehouse or fulfillment?
Fulfillment pays off for growing online stores that don't want to deal with premises, staff and seasonal peaks. Your own warehouse with a WMS makes sense when packaging is part of your brand, your products are specific or you already have a warehouse and team. Fulfillment has variable costs, your own warehouse has fixed costs.
What do FIFO and FEFO mean in a warehouse?
FIFO (first in, first out) means the goods that arrived first leave the warehouse first. FEFO (first expired, first out) means the goods with the nearest expiry date leave first. FEFO is important for food, cosmetics and supplements, and a WMS enforces it automatically.
Need to connect your warehouse to your online store?
We'll connect your WMS, carriers and accounting with your Shopify store, or build a custom warehouse system where an off-the-shelf solution isn't enough. Take a look at our app development services or book a free consultation.
Sources
- SAP: Leader in 2025 Gartner Magic Quadrant for WMS
- Oracle: Leader in 2025 Gartner Magic Quadrant for WMS
- Blue Yonder: Leader in 2025 Gartner Magic Quadrant for WMS
- Infios: Leader in 2025 Gartner Magic Quadrant for WMS
Author: Miroslav Volovec, CEO of 3NODE Software s.r.o. – specialists in e-shop and app development on the Shopify platform.
