What to Do If You Sell Both FBA and Non-FBA Products on Shopify

So you’ve got some products that are fulfilled by Amazon and other products that are fulfilled by you or another service. How the heck do you set up your shipping and fulfillment services so that the right orders go to the right place? And what about mixed orders? How do you handle partial fulfillment?

I gotchu fam.

Setting up Shopify shipping rates

There are two parts to the puzzle:

+ Fulfillment service

+ Shipping rates

Fulfillment Service

The first part is pretty straightforward. If you’re using the FBA Shipping app to manage your FBA products, set the fulfillment service to “FBA Shipping” on those products. The fulfillment service for your other products should be set to “Shopify” or whatever other fulfillment service you have set up.

Shopify fulfillment service

First part, done. Now the shipping rates. This is where it gets a little tricky.

Shipping Rates

You’ll set up shipping rates for your FBA products in the FBA Shipping app. And you’ll set up shipping rates for your other products in your Shopify shipping settings.

Amazon is super nit-picky about what shipping rates they’ll accept. Amazon WILL NOT accept orders that use shipping rates from your Shopify shipping settings. They only accept the shipping rates from the FBA Shipping app (we’re BFFs).

Amazon BFF

That means if a customer is buying FBA products and they select a Shopify shipping rate at checkout, Amazon will reject the order. And even though we’re BFFs with Amazon, we can’t make them accept it. So your customer will be unhappy which will make you unhappy which will make your friends and family unhappy and the whole world will end up unhappy. We don’t want that!

So the goal is to prevent those Shopify shipping rates from pulling through to the checkout when customers order FBA products. You do that by telling Shopify that your manually fulfilled products are really heavy and setting the weight ranges for the shipping rates to correspond to those heavy weights.

When you do this correctly, the weights of your Amazon products won’t line up with your weight based rates. So when a customer buys an FBA product, only Amazon’s rates will show at checkout, not your weight based rates.


I sell free-range hairbrushes through FBA. They all weigh less than a pound. I also sell touchscreen shampoo, for which I fulfill the orders.

My shampoo doesn’t weigh much more than my hairbrushes, but I’m going to tell Shopify that it does. So the first thing I do is change the weights for all of my shampoo to 25 pounds.

Shopify weights

Now I’m going to set up weight based shipping rates. To keep it simple, I want to charge $5 shipping for one bottle of shampoo and $8 shipping for two or more bottles. Here’s how I set that up:

+ Set up a weight based shipping rate for 25-26 pounds for $5 (One bottle = 25 pounds).

+ Set up a second weight based shipping rate for 50-5000 pounds for $8 (Two bottles = 50 pounds).

Super duper important: You have to name your weight based rates the same thing as Amazon’s rates. Otherwise, Shopify will see a conflict and your shipping rates won’t work. Amazon’s rate names are:

+ Standard

+ Expedited

+ Priority

Just like that, with the first letter capitalized and no extra letters or words.

Shopify weight based rates

So my hairbrush shipping rates are already set up in the FBA Shipping app. Now let’s see how this will play out.

What Happens at Checkout

Customer goes to checkout with one hairbrush in their cart:

+ Shopify sees that the weight is less than a pound, so it only pulls in the FBA Shipping rates. The product weight doesn’t meet the minimum 25 pounds for a weight based shipping rate to kick in.

Customer goes to checkout with one bottle of shampoo in their cart:

+ Shopify sees the weight is 25 pounds and the fulfillment service is “Shopify.” They pull in the $5 weight based rate and NO Amazon rates.

Customer goes to checkout with 7 bottles of shampoo in their cart:

+ Shopify sees the weight is 175 pounds (7 x 25 pounds each) and the fulfillment service is “Shopify.” They pull in your $8 weight based rate (total weight is between 50 and 5000 pounds) and NO Amazon rates.

Customer goes to checkout with one hairbrush and one bottle of shampoo in their cart:

+ Shopify sees a “Standard” rate from Amazon for the hairbrush and a “Standard” rate from Shopify for the shampoo. The won’t pull in both rates, instead they’ll just pull in the Shopify rate. So your customer will be charged $5 for shipping. You’re still on the hook to pay Amazon shipping, but you can factor that into your pricing. The important thing is that Amazon still sees a shipping rate they like (Standard), so they fulfill their portion of the order while you fulfill your portion.

Okay, what if I want to offer free shipping for orders over $25?

For your FBA products, you’ll set that up in the FBA Shipping app.

FBA Shipping app free shipping

For your manually fulfilled products, you’ll still need those weight based rates. But how do you set up price based rates using weight based rates? Sounds confusing. But it’s actually pretty simple.

Let’s say my shampoo is priced at $12. A customer would need to buy 3 bottles to qualify for free shipping, right? 2 bottles x $12 = $24, so no free shipping. 3 bottles x $12 = $36, so yes free shipping.

I just need to adjust my weight based rates. Here’s what I’ve already got:

+ 25-26 pounds (one bottle) for $5

+ 50-5000 pounds (2+ bottles) for $8

So I’ll update my second rate to be 50-51 pounds for $8. Then set up a new rate to be 75-5000 pounds for free.

Shopify weight based shipping rates 2

Now customers will pay $5 shipping for one bottle, $8 shipping for two bottles and free shipping for three or more.


It can be a bit tricky to wrap your brain around weight based shipping rates, so make sure you’ve had your coffee before attempting this. If it still gives you a headache, get in touch with us. We’ve helped tons of stores set this up, so we can get you up and running quickly and painlessly.

About the Author

Gennifer is the Marketing Manager at ByteStand, where she lives and breathes customer service education while sipping coffee in her pajamas.

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