How to Migrate to Shopify POS Without Losing Data or Sales

Switching to a new POS system can feel overwhelming. I’ve been in eCommerce for over a decade, and I’ve seen countless businesses struggle with POS migrations—inventory mismatches, lost customer data, and payment processing nightmares.

But here’s the truth: Migrating to Shopify POS doesn’t have to be a headache. If you follow the right steps, you can move your business over smoothly, keep your sales running, and even improve your operations.

This guide will walk you through exactly how to migrate to Shopify POS—without breaking your business in the process.

Why Migrate to Shopify POS?

If you’re reading this, you’re probably frustrated with your current POS system. Maybe it’s outdated, too expensive, or just doesn’t sync well with your online store. I’ve worked with countless business owners who struggle with:

Inventory mismatches – Selling a product in-store, only to find out it was already sold online.
Slow checkouts – Long wait times at the register due to an outdated system.
Lack of integration – Having to manually update stock and customer details across platforms.
High transaction fees – Losing profit on every sale due to expensive payment processing.

If any of this sounds familiar, you’re not alone. Most traditional POS systems weren’t built to seamlessly connect with eCommerce stores. That’s where Shopify POS changes the game.

Key Benefits of Shopify POS

All-in-One System

Tired of juggling multiple platforms for online and in-store sales? Shopify POS syncs everything in real time, so your business runs smoothly without extra work.

With Shopify POS, you get:

A centralized system that tracks both online and in-store orders.
Automatic inventory updates—no more manual stock adjustments.
Seamless customer profile integration across all sales channels.

If a customer buys something online, your store inventory updates immediately. If someone purchases in-store, your Shopify website reflects the change instantly. No more overselling or frustrating stock issues.

Better Inventory Management

Running out of stock? Shopify POS prevents overselling and keeps your inventory accurate at all times.

What Shopify POS does for inventory:

Real-time stock syncing across online and retail locations.
Multi-location inventory tracking, so you can move products between stores effortlessly.
Low-stock alerts, so you always know when it’s time to reorder.

If you operate multiple stores, Shopify POS lets you transfer inventory between locations in just a few clicks. No more manual spreadsheets or stock confusion.

Lower Payment Processing Fees

If you’re using a third-party POS, chances are you’re paying extra fees on every sale. Shopify POS integrates with Shopify Payments, which can lower your transaction costs significantly.

Compare the fees:

Square & Lightspeed: 2.6% – 2.9% per transaction.
Shopify Payments: As low as 2.4% per transaction (depending on your Shopify plan).

By switching to Shopify Payments, you eliminate third-party processing fees and simplify your payment system. Plus, you get faster payouts directly to your bank account.

Seamless Customer Experience

Today’s customers expect a frictionless shopping experience, whether they buy online or in-store. Shopify POS ensures that all customer interactions are connected, making returns, exchanges, and loyalty rewards effortless.

With Shopify POS, you can:

Track purchase history across both online and in-store transactions.
Offer personalized discounts based on previous shopping behavior.
Accept in-store returns for online purchases (and vice versa).

For example, if a customer buys a pair of shoes online but wants to exchange them in-store, Shopify POS automatically pulls up their order history, allowing you to process the exchange in seconds.

If your current POS system is holding you back, it’s time to switch. Shopify POS eliminates manual work, lowers fees, and creates a seamless customer experience.

No more inventory headaches
Faster checkout process
Lower payment processing costs
A unified system for online & in-store sales

Migrate to Shopify POS Without Losing Data or Sales – Step by Step

Let’s go over exactly how to migrate to Shopify POS the right way.

Step 1: Choose the Right Shopify POS Plan

Before you migrate, you need to pick the right Shopify POS plan based on your business size, sales volume, and operational needs. Shopify offers two versions of its POS system: Shopify POS Lite and Shopify POS Pro.

While both allow you to process in-store sales and accept payments, the features and capabilities differ significantly.

If you’re running a small retail store, pop-up shop, or occasional in-person sales events, Shopify POS Lite may be enough. But if you need real-time inventory tracking, multiple store locations, and advanced reporting, then Shopify POS Pro is a better fit.

Let’s break down both options:

Shopify POS Lite (Free with Shopify Plans)

✔️ Included with all Shopify subscription plans (Basic, Shopify, Advanced, and Plus).
✔️ Basic in-store sales tools, including barcode scanning and product lookups.
✔️ Works well for pop-ups, small retail setups, and businesses with simple in-store operations.

Shopify POS Lite is a great option for businesses that primarily sell online but occasionally do in-person sales at markets, trade shows, or pop-up events.

It gives you the ability to accept card payments, manage inventory, and process sales without requiring a separate POS system. However, if you run a full-fledged brick-and-mortar store, this version may lack the advanced features needed to scale your operations.

Shopify POS Pro ($89/month per location)

✔️ Advanced inventory tracking – Monitor stock levels in real time across multiple locations.
✔️ Multi-location support – Perfect for businesses with multiple retail stores or warehouses.
✔️ In-store pickup & local delivery – Offer customers flexible shopping options.
✔️ Staff roles & permissions – Control employee access based on their role.

Shopify POS Pro is designed for retailers who need a fully integrated, data-driven system. It allows you to track inventory across multiple stores, manage in-store pickup orders, and provide seamless customer service by syncing online and offline sales.

Additionally, the staff management feature helps ensure that employees only have access to the tools and data relevant to their role.

If you operate a physical store with high sales volume, Shopify POS Pro is definitely worth the investment.

The ability to track sales trends, monitor performance, and adjust stock levels in real time gives you a competitive edge and prevents common retail challenges like overselling or stock discrepancies.

Which Plan Should You Choose?

If you're just starting out and your physical sales are minimal, Shopify POS Lite can be a good starting point.

But if you’re serious about scaling your retail operations, offering in-store pickup, multi-location management, and advanced analytics, then POS Pro is the way to go.

Pro Tip: Shopify POS Pro is charged per location, so if you have multiple stores, factor that into your costs when deciding on a plan.

Once you've selected the right Shopify POS plan for your business, the next step is to export your data and prepare for the migration process. Let’s go over that next.

Step 2: Export Data from Your Current POS System

One of the biggest mistakes I see businesses make during a POS migration? Not backing up their data properly before switching systems.

Losing product listings, customer records, or sales history can cause major disruptions, leading to inventory issues, unhappy customers, and revenue loss.

To avoid this, you need to export all critical business data from your existing POS system before making the switch. This ensures that nothing gets lost during the transition and allows you to easily import everything into Shopify POS.

Here’s what you need to export:

Products & Inventory – Includes SKUs, product names, descriptions, pricing, and stock levels. This is essential to keep your inventory accurate when switching systems.
Customers – Names, email addresses, phone numbers, and purchase history. Retaining customer data allows for seamless loyalty programs, personalized marketing, and accurate order tracking.
Sales History – Past transactions, order numbers, and payment records. While Shopify POS doesn’t allow direct sales history imports, keeping a record ensures you have access to past transactions if needed.
Gift Cards & Discounts – If you offer store credit or run promotions, ensure these are accounted for so customers don’t lose their balances.

If your current POS system allows you to export this data in CSV format, that’s ideal—since Shopify POS supports CSV uploads for easy migration.

How to Export Data from Common POS Systems

Each POS system has a different method for exporting data. Here’s how to do it for some of the most common platforms:

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Square: Go to Reports > Sales Summary > Export CSV to download transaction data. For inventory, use Items > Actions > Export Library.
Lightspeed: Use the Inventory Manager to download a product list. For customer and sales data, navigate to Reports > Export Data.
Clover: Access the Transactions Export Tool in your Clover Dashboard to download sales records. Inventory can be exported from the Inventory App.
Vend: Navigate to Products > Export All to download inventory data. Customer and sales reports can be exported from the Reporting section.

If your POS system isn’t listed here, check your provider’s support documentation or contact their customer service for guidance on exporting data.

What to Do After Exporting Your Data

Once you’ve successfully exported everything, don’t rush into uploading it to Shopify just yet. Take the time to:

Review and clean up your data – Look for duplicates, outdated information, and errors. Ensuring accuracy before importing will save you time later.
Save multiple backup copies – Store your exported files on an external drive, cloud storage, and a local device in case something goes wrong.
Verify exported formats – Shopify POS works best with CSV files, so check that your data is properly formatted for a smooth import.

A clean, accurate data transfer is key to making the transition to Shopify POS as smooth as possible. Once your data is backed up and organized, you’re ready for the next step—importing everything into Shopify POS.

Step 3: Import Your Data into Shopify POS

Once you’ve exported all your data from your previous POS system, it’s time to import everything into Shopify POS. This step is crucial—errors here can lead to missing products, inaccurate inventory counts, and customer profile issues.

Before importing, double-check that your files are formatted correctly. Shopify supports CSV file uploads, so make sure your product, inventory, and customer data are structured properly. If needed, use Shopify’s sample CSV templates to clean up your data before uploading.

1. Import Products & Inventory

Your inventory is the backbone of your store, so this needs to be 100% accurate when migrating. Shopify allows bulk product imports via CSV, making it easy to upload everything at once.

How to import products into Shopify:

Go to Shopify Admin > Products > Import.
Upload your CSV product file and review the data before submitting.
Shopify will process the file and add your products to the store.

Pro Tip: Always double-check SKU numbers, pricing, and inventory counts before finalizing the import. If there are errors in your product file, they can cause stock discrepancies and pricing issues down the line.

2. Transfer Customer Data

Instead of manually entering each customer one by one, use Shopify’s bulk customer import tool to save time.

How to import customer data:

Go to Shopify Admin > Customers > Import customers.
Upload your CSV file containing customer names, emails, and purchase history.
Shopify will automatically create customer profiles based on the imported data.

This step is crucial if you offer loyalty programs, customer discounts, or personalized marketing. Keeping past purchase data allows you to deliver a seamless experience for returning customers.

3. Migrate Sales & Transaction History

Shopify POS does not allow direct imports of past transactions, but there are workarounds to retain historical data for reporting and customer service purposes.

How to handle old sales records:

Manually enter past orders for high-value or recent transactions.
Keep old POS data stored externally for reporting and tax purposes.
Use a third-party app like Xporter Data Export to sync historical sales data.

If you need access to past sales trends and analytics, consider keeping your old POS system active in a limited capacity or exporting reports before shutting it down.

Step 4: Set Up Your Shopify POS System

With your data successfully imported, it’s time to configure Shopify POS to match your business needs.

1. Connect Shopify POS to Your Store

First, you need to install the Shopify POS app on your preferred device. Shopify POS works best on iPads, tablets, and mobile devices, but you can also use it on desktop systems with compatible hardware.

How to set up Shopify POS:

Download the Shopify POS app from the App Store or Google Play.
Log in using your Shopify credentials.
The system will sync with your Shopify store, pulling in products, inventory, and customer data automatically.

2. Set Up Your Payment Methods

Shopify Payments is the default payment processor, but you can also add alternative payment options depending on your business model.

Available payment methods in Shopify POS:

Shopify Payments (credit/debit cards, Apple Pay, Google Pay)
PayPal
Manual payments (cash, bank transfers)
Third-party gateways like Stripe or Square

If you process a high volume of transactions, compare transaction fees to see which provider offers the best rates for your business.

3. Sync Inventory Across Locations

If you operate multiple stores, you need to assign inventory correctly to each location.

How to manage inventory locations in Shopify:

Go to Shopify Admin > Locations.
Add all physical store locations.
Ensure that each product has the correct stock levels assigned to each store.

Now, whenever a product is sold in-store or online, Shopify automatically adjusts the inventory in real time, preventing overselling and stock discrepancies.

4. Test Transactions Before Going Live

Before you fully launch Shopify POS, run a few test transactions to make sure everything is working correctly.

Key things to check:

Process a test sale using Shopify POS.
Refund a transaction to confirm return policies work properly.
Check inventory updates to ensure stock levels adjust in real time.

If you notice any errors, fix them now before your store goes live to avoid issues with real customers.

Step 5: Train Your Staff on Shopify POS

Switching to a new POS system means your employees will need training to handle sales, refunds, and inventory management effectively.

Key areas to train your staff on:

Processing sales & refunds – How to handle transactions smoothly.
Using discounts & promo codes – Applying customer incentives at checkout.
Managing customer profiles – Searching purchase history and issuing rewards.
Inventory checks & stock updates – Ensuring products are available in the right locations.

Shopify offers video tutorials within the POS dashboard, making it easy for employees to learn the system quickly. If you run a busy retail store, consider holding a hands-on training session before going live.

Step 6: Post-Migration Testing & Troubleshooting

Once everything is set up, don’t rush into full operations just yet. Even if the migration process went smoothly, there’s always a chance that small errors could cause big problems down the line. Before you officially switch over, take a few days to test Shopify POS in a controlled environment to ensure that everything works as expected.

Skipping this step can lead to inventory discrepancies, payment failures, or missing customer data, which can frustrate both your team and your customers. A few days of careful testing now can prevent major operational headaches later.

Common Issues to Check For:

Missing customer data – Some profiles may not transfer perfectly. Check for duplicates or incomplete records.
Inventory mismatches – Run a full stock audit to verify that Shopify’s inventory matches your actual stock levels.
Payment processing errors – Test different payment methods (credit cards, cash, and digital wallets) to ensure seamless transactions.

If any issues come up, fix them before fully switching over. A smooth transition ensures that customers won’t experience any disruptions, and your team will be confident using the new system.

Once testing is complete, you’re officially ready to start selling with Shopify POS.

Final Thoughts

If your current POS system is holding you back, it’s time to make a change.

Whether you're struggling with inventory mismatches, slow checkouts, high transaction fees, or disconnected online and in-store sales, Shopify POS solves these problems by bringing everything into one seamless system.

For retailers, efficiency is everything. A disorganized POS system doesn’t just slow down operations—it can lead to lost sales, frustrated customers, and unnecessary costs.

Shopify POS helps you streamline your entire business, making it easier to manage inventory, track customer data, and process transactions without the usual headaches.