How to Set Up an Order Management System (OMS) That Scales With Your Ecommerce Business

Still using spreadsheets to manage orders? It’s time to upgrade.

As your ecommerce business grows, the complexity of managing orders across multiple sales channels increases exponentially. One-off fixes, like juggling spreadsheets, manually updating stock levels, or copy-pasting shipping addresses, might’ve worked when you were just starting out. But now, they’re costing you time, sales, and customer trust.

Enter the Order Management System (OMS), a centralized, automated system that brings order processing, inventory tracking, and fulfillment under one roof.

This guide walks you through:

• What an OMS does and why it’s essential

• Step-by-step setup instructions

• Order management best practices

• Tips to automate and future-proof your operations

Bottom line: A smart OMS is your growth engine. Let’s get it set up right.

What Is an Order Management System (OMS)?

An Order Management System is a centralized platform that tracks, processes, and fulfills orders from multiple sales channels, automatically and in real time.

Instead of bouncing between Shopify, Amazon, eBay, spreadsheets, and emails, your OMS keeps everything in sync, streamlining your entire order process from purchase to delivery.

Here’s what a good OMS does for you:

• Avoids order errors: No more duplicates, lost orders, or missed shipments

• Syncs inventory in real time: Keep stock levels consistent across all channels

• Speeds up fulfillment: Orders are routed automatically to the best warehouse

• Reduces manual work: Say goodbye to spreadsheets and human error

Want a detailed breakdown on how to choose the right software for your business? Check out our post Which Inventory Management Software Should I Use for My Ecommerce Store?

Why You Shouldn’t Run Your Business Without an OMS

Still running things manually? That’s a recipe for:

• Lost or duplicate orders: Leads to refunds, unhappy customers, and lost revenue

• Inventory mismatches: You oversell products you don’t actually have in stock

• Slow fulfillment: Late deliveries = bad reviews and lower customer retention

• Time-consuming workflows: Managing orders in spreadsheets takes hours

If you want to scale your business without scaling your headaches, a smart OMS is non-negotiable.

Step-by-Step Guide: How to Set Up Your Order Management System

Step 1: Choose the Right OMS for Your Ecommerce Workflow

Before you do anything else, you need the right foundation. And not all order management software is built for the demands of mid-market ecommerce.

An OMS isn’t just a dashboard, it’s the nerve center of your operations. It connects your sales channels, syncs inventory in real time, routes orders to the right warehouse, generates shipping labels, tracks fulfillment, and keeps customers informed.

What to Look For in a Best-in-Class OMS:

• Seamless integrations with Shopify, Amazon, Walmart, eBay, and more

• Real-time inventory syncing to prevent overselling and stockouts

• Automated order routing to fulfill faster and cut shipping costs

• Multi-carrier support for FedEx, UPS, USPS, DHL, etc.

• Scalability to handle growth without disrupting operations

Pro Tip: Don’t settle for a tool that “kinda works.” If you’re having to hack together solutions or babysit your software, it’s time to upgrade.

How to Evaluate Order Management Software:

• Read reviews on platforms like G2 and Capterra to spot real-world red flags

• Ask about automation. How deep does it go? Can it scale?

• Request a demo so you can explore the platform before committing

• Think long-term. Will this software grow with your team, your SKUs, and your sales channels?

Want to skip the guesswork?
Ecommerce brands like Jeannie N Mini and DJ Direct chose Goflow to simplify complex, high-volume operations, and saw massive improvements in speed, accuracy, and customer satisfaction.

Step 2: Connect All Your Sales Channels

Once you’ve selected your OMS, the next move is to connect every sales channel you sell on. This is what transforms your OMS from a passive system into a powerful command center.

A proper multi-channel order management setup includes:

• Shopify, WooCommerce, Amazon, Walmart, eBay, Etsy, and other marketplaces

• Direct website orders and wholesale channels

• POS systems or third-party selling tools

When these platforms are integrated into your OMS, it eliminates the lag between when an order is placed and when your team sees it. Orders are automatically pulled into a centralized dashboard, where fulfillment rules, inventory sync, and tracking updates happen in real time.

Key setup actions:

• Enable two-way sync between your OMS and each channel

• Set rules for how data flows. e.g., cancellations, returns, and out-of-stock items

• Validate SKU matching across platforms to avoid inventory mismatches

Without real-time syncing, you’re flying blind. That’s how you oversell products you don’t have in stock, or worse, miss entire orders. For more info, check out our blog post How Do I Get Started With Inventory Management?

Step 3: Migrate or Input Existing Order Data

Whether you’re migrating from spreadsheets or moving away from a clunky, outdated tool, the transition is a one-time lift that pays off long-term.

If you're switching from spreadsheets:

• Export your order history and customer data

• Format to match your OMS’s import template

• Use the bulk upload feature. Most modern systems support CSV import

If you’re starting fresh:

• Manually enter your current inventory and open orders

• Set up product SKUs, categories, and warehouse locations

• Establish basic automation rules (e.g., shipping speed by region or product line)

This is where clean data matters.
The more accurate your initial setup, the fewer issues you’ll encounter when orders start flowing in. Take the time to set a strong foundation now to avoid slowdowns and corrections later.

Need more help? This post on automation in inventory management can help you streamline your backend before migrating.

Step 4: Configure Fulfillment and Routing Rules

Fast, error-free fulfillment is one of the biggest advantages of a modern OMS. But to get there, you need smart rules in place.

Set up rules for:

• Which warehouse or 3PL fulfills which orders (based on location, product type, or urgency)

• Shipping methods (standard vs. expedited, cost-based routing, etc.)

• Backup routing for stockouts or carrier delays

• Packaging logic (e.g., bundle SKUs, fragile items, or size constraints)

Why it matters:
Manual decision-making slows you down and introduces human error. With smart routing in place, your system handles the logic automatically, no more bottlenecks when order volume spikes.

Want to reduce shipping delays and stockouts? Master stock rotation methods like FIFO, LIFO, and FEFO.

Step 5: Set Up Real-Time Tracking and Customer Notifications

Today’s customers expect visibility. If your order tracking system is delayed or unclear, it erodes trust, fast.

Your OMS should:

• Automatically generate tracking numbers and send them to customers

• Send status updates via email or SMS (confirmation, shipping, delivery)

• Surface live dashboards so your team can track every order at a glance

• Trigger alerts for failed deliveries or returns in real time

Smart Order Followups can help you streamline post-shipment follow ups by letting you detect, track and manage any post-shipment issues. With intuitive workflows and guided on-screen steps, you can ensure that every order is recognized as ‘shipped’ and invoiced, minimizing customer complaints and safeguarding your account health KPIs. Learn more about how they work here. 

Step 6: Test Everything Before You Go Live

A failed rollout can wreak havoc. Before switching fully to your new OMS, simulate real-world scenarios to make sure everything works as expected.

Testing checklist:

• Place test orders through every connected channel

• Verify order syncing, routing, and tracking updates

• Review order confirmation emails and delivery notifications

• Confirm inventory adjusts in real time across all platforms

• Train your team on workflows, dashboards, and exception handling

• Have a rollback plan just in case something goes wrong

Even the best systems need stress-testing before launch. This ensures that once you’re live, everything runs smoothly under pressure, whether you’re processing 10 orders or 10,000.

Order Management Best Practices for Long-Term Success

Once your OMS is up and running, don’t set it and forget it. The most efficient ecommerce operations are constantly evolving, and your OMS should evolve with them.

1. Audit your order data regularly

• Spot delays, routing errors, or missed SLAs

• Identify system bottlenecks before they escalate

• Review return rates and fulfillment speed by channel or warehouse

2. Standardize your data inputs

• Use consistent naming conventions, SKUs, and shipping methods

• This improves reporting, automation, and accuracy at scale

3. Optimize for multichannel selling

• Align pricing and inventory across channels

• Automate updates so your stock levels are always accurate

• Avoid overselling or frustrating customers with inconsistent information

4. Automate wherever possible

• Set rules for low-stock alerts and restock triggers

• Use historical data for demand forecasting

• Automate common workflows like backorder communication or split shipments

Automation isn’t just a nice-to-have, it’s essential infrastructure for modern ecommerce.

If you're ready to go deeper on this topic, don’t miss our post: Work Smarter, Not Harder: The Power of Automation for Inventory Management. It breaks down exactly how automation can streamline your inventory processes, reduce errors, and help you scale with confidence.

5. Revisit Your OMS Configuration Every 6–12 Months

Your business evolves. So should your system.

• Adjust fulfillment rules based on order volume

• Add new warehouses, channels, or shipping partners

• Review automation rules to keep things efficient

For more smart ways to optimize your inventory management, check out our guide: Take Control of Your Stock: 10 Inventory Management Best Practices. 

Final Thoughts: Your OMS Is a Growth Lever. Use It That Way

An Order Management System isn’t just about saving time, it’s a strategic tool for scaling your ecommerce business. The right setup helps you eliminate manual work, reduce fulfillment errors, and deliver a smoother customer experience across every channel.

If your current setup can’t keep up, it’s time for something smarter.

See how Goflow helps fast-growing brands centralize, automate, and scale their operations, without the chaos.
Book a free demo and take control of your ecommerce order management today.