Selling on one platform is simple. You get an order, you print a label, you ship it. But the moment you add a second or third sales channel, shipping becomes a logistical headache that scales worse than you'd expect.
We hear from sellers all the time who are managing Shopify orders in one browser tab, Amazon Seller Central in another, and eBay's Seller Hub in a third. They're cross-referencing inventory on a spreadsheet, manually entering tracking numbers, and occasionally sending the wrong item to the wrong customer because everything is fragmented.
If that sounds like your Tuesday afternoon, here's how to fix it.
The Multi-Channel Shipping Problem
Each marketplace has its own fulfillment requirements, shipping timelines, and metric systems. Here's what you're dealing with:
Amazon FBM expects you to ship within 1-2 business days depending on the category. Late shipments tank your seller metrics and can get your account suspended. Amazon also requires specific carrier integrations for tracking to register properly.
eBay has its own shipping requirements. You need to upload tracking within your stated handling time or risk "item not shipped" defects. eBay also has specific policies about which carriers' tracking numbers they accept.
Shopify is more flexible on timing (it's your store, your rules), but customers expect fast shipping. And if you're offering free shipping on Shopify but charging on eBay, you need to manage that pricing inconsistency.
When you're doing 50 orders a day across three platforms, manually logging into each one to print labels and update tracking isn't just tedious — it's a guaranteed way to make mistakes.
Why You Need a Centralized Shipping Tool
A multi-channel shipping platform connects to all your sales channels, pulls every order into one dashboard, and lets you process everything from a single interface. Here's what that actually looks like in practice:
- Orders from Shopify, Amazon, eBay (and Walmart, Etsy, wherever else you sell) flow into one queue
- You can sort, filter, and batch select orders
- The tool rate-shops across carriers and presents the cheapest options
- You print all labels in one batch — 30 Shopify labels, 15 Amazon labels, and 8 eBay labels at once
- Tracking numbers automatically sync back to each marketplace
- Inventory quantities update across all channels when an item ships
That last point is critical. Without inventory sync, you sell the last unit on Shopify and eBay simultaneously, and now you're canceling an order and getting a defect on one of your accounts.
The Three Best Multi-Channel Shipping Tools
ShipStation
ShipStation is the most popular multi-channel shipping solution, and for good reason. It connects to over 100 selling channels and marketplaces, including Shopify, Amazon, eBay, Walmart, Etsy, WooCommerce, and BigCommerce.
What makes it stand out:
- Automation rules that apply actions based on order criteria (e.g., "All Amazon orders under 1 lb use USPS Ground Advantage, all eBay orders over 2 lbs use UPS Ground")
- Batch label printing across all channels
- Custom packing slips per channel (you probably don't want your Shopify branding on an Amazon order)
- Discounted USPS, UPS, and FedEx rates built in
- Detailed reporting broken down by channel, carrier, and product
Pricing: Starts at $9.99/month for 50 shipments. The Growth plan at $29.99/month handles 500 shipments and includes automation. High-volume plan at $159.99/month handles up to 7,500 shipments.
Best for: Sellers doing 100+ orders/month across 2+ channels who want strong automation.
Ordoro
Ordoro is less well-known than ShipStation but has a loyal following among sellers who need inventory management alongside shipping. It's particularly strong at keeping inventory counts synchronized across multiple channels.
What makes it stand out:
- Deep inventory management with automatic quantity syncing
- Dropshipping support (route orders directly to suppliers)
- Kitting and bundling support
- Purchase order management
- Supplier management tools
Pricing: The shipping-only plan starts at $59/month, which includes access to discounted rates and multi-channel order management. Plans that include inventory management and automation start higher.
Best for: Sellers who need inventory management as much as they need shipping tools, or who do dropshipping alongside stocked products.
Veeqo (by Amazon)
Veeqo is Amazon's own multi-channel shipping software, and here's the kicker: it's completely free. Amazon acquired Veeqo in 2021 and removed the price tag to encourage sellers to use it.
What makes it stand out:
- 100% free — no monthly fee, no per-label fee
- Direct Amazon integration (obviously very strong)
- Connects to Shopify, eBay, Etsy, WooCommerce, and others
- Inventory sync across all channels
- Discounted USPS, UPS, DHL, and FedEx rates
- Warehouse management features
Pricing: Free. Seriously.
Best for: Amazon-centric sellers who want a free tool and don't need the deep automation rules that ShipStation offers.
Setting Up Your Multi-Channel Workflow
Here's how we recommend configuring your centralized shipping system, regardless of which tool you choose:
Step 1: Connect All Channels
Link every platform where you sell. This includes your Shopify store, Amazon Seller Central, eBay, Etsy, and any others. Most tools use OAuth or API keys for this — follow the setup wizard and you'll be connected in a few minutes per channel.
Step 2: Set Up Automation Rules by Channel
This is where the real time savings come from. Create rules that handle the repetitive decisions:
- Amazon FBM orders under 1 lb: Auto-assign USPS Ground Advantage, auto-select smallest poly mailer preset
- eBay orders, any weight: Rate-shop between USPS and UPS, pick cheapest
- Shopify orders with "Free Shipping" tag: Use USPS Ground Advantage for orders under 1 lb, UPS Ground for everything else
- All orders over $100: Add signature confirmation
- International orders: Route to Easyship integration or apply customs form template
These rules run automatically when orders come in. On a good day, you open your shipping dashboard, 80% of orders are already pre-configured with the right carrier, service, and package type. You just review and hit print.
Step 3: Configure Package Presets
Define your box sizes and packaging types in the software. Instead of typing dimensions every time, you'll select "Small Box" or "Poly Mailer" from a dropdown. Good presets to start with:
- Poly Mailer (10x13")
- Small Box (8x6x4")
- Medium Box (12x10x6")
- Large Box (16x12x8")
- Padded Flat Rate Envelope (USPS)
Step 4: Set Up Inventory Sync
Turn on inventory syncing so that when you sell an item on Shopify, the quantity decreases on eBay and Amazon too. This prevents overselling, which is one of the fastest ways to get performance defects on Amazon and eBay.
A word of caution: set a buffer. If you have 10 units in stock, consider syncing 8 across your channels. This gives you a small safety net for timing delays between when an order comes in and when inventory levels update.
Step 5: Create Channel-Specific Packing Slips
Amazon doesn't want you putting Shopify flyers in their orders, and your Shopify customers don't want a packing slip that looks like it came from a marketplace seller. Most multi-channel tools let you create different packing slip templates per channel with appropriate branding.
A Real Daily Workflow
Here's what a typical morning looks like for a seller doing 40-60 orders per day across Shopify, Amazon, and eBay, using ShipStation:
8:00 AM — Open ShipStation. Orders from overnight have already been imported and automation rules have pre-assigned carriers and package types to most of them.
8:05 AM — Review the order queue. Filter by "Awaiting Shipment." Check that automation rules assigned correctly. Manually adjust any outliers (unusual package sizes, customer notes requesting specific carriers).
8:15 AM — Select all orders, click "Create Labels." ShipStation batch-prints 45 labels in about 90 seconds.
8:20 AM — Pull products, match them to packing slips (printed alongside labels), pack boxes, apply labels. This is the physical work and takes the most time.
9:30 AM — All packages staged for carrier pickup. Tracking numbers have already synced back to Shopify, Amazon, and eBay automatically.
Total time managing the shipping software: about 15 minutes. The rest is physical packing. Compare that to logging into three separate platforms, rate shopping manually, copying tracking numbers between tabs, and hoping you don't mix up an order.
Common Pitfalls to Watch For
Over-syncing inventory. If one channel cancels an order, make sure your tool restores the inventory count. Not all tools handle cancellations and returns gracefully.
Different handling times per channel. Amazon might require same-day shipping on some products. Your Shopify store might promise 2-day handling. Configure your automation rules to prioritize Amazon orders in the queue.
Carrier restrictions per marketplace. Amazon has specific requirements for which carriers qualify for valid tracking. Make sure your carrier choices meet each platform's requirements, or you'll see "tracking not valid" flags on your account.
The "one more channel" trap. Adding Walmart Marketplace or TikTok Shop sounds great, but each channel adds complexity. Make sure your shipping workflow can handle it before expanding, or you'll end up right back in tab-switching chaos.
Multi-channel selling is where the real growth happens for most e-commerce businesses. Getting shipping right is what makes that growth sustainable instead of just more stressful.