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Marketplace Showdown: Shopify vs Amazon, Which Should You Be Focusing On?

In the great debate of who is better, Amazon vs Shopify, learn how you can integrate Shopify into you process and leverage both platforms.
10 minutes read

Expanding beyond Amazon is a heavily debated topic. Even among the most successful sellers the consensus is not uniform. Many say that shifting focus away from the ease and reliability of the Amazon platform is a suicide mission. Still, some, often fed up with Amazon’s apparent lack of concern for the well-being of third party sellers and their wanton disregard for their own policies, advocate for early and aggressive implementation of non-Amazon strategies.

Both sides have great arguments, and while the number of Amazon-only success stories far outshine those of off-Amazon fame, it is hard to argue that off-Amazon brands that have “made it” have done so in bigger ways than most private labelers could even dream.

So who is right? Which path should you take?

Do you spend the time, energy and money building out an off-Amazon presence?

Or continue single-minded focus on Amazon until you’ve gained decent success?

I’m here to present to you a third option…

Why Not Do Both?

why not both?

What if I told you there was a relatively simple path to achieving both goals?

Rather than have a custom site built and finding a third party fulfillment center (or even building your own), you can continue to sell your FBA inventory while expanding your reach beyond the confines of the Amazon platform.

But how? You might be asking…

With Shopify.

Before we get into the logistics of how this works, lets go over why you might even want to consider doing this.

Well, first and foremost, it isolates your message. See, when your products only live on Amazon, then only Amazon shoppers will see them. Now, don’t get me wrong, this is a big portion of the population, but the major downside to that is that these potential customers also see all of your competitors.

But on your own site, not only are you expanding your reach beyond Amazon, but you are also isolating your message so that shoppers only see your products and their benefits.

Another big benefit is Google Shopping Ads. If you have a catalog uploaded from Shopify to Google Merchant Center, you can run Shopping ads that will drive sales (sometimes even at a profit 😁).

And then there’s the sales funnel and upsell/downsell capabilities. If you are a believer in the power of sales funnels, then you should be aware that e-Comm legend Ezra Firestone offers a Shopify app called “One Click Upsell” that facilitates up and down-sells for your product pages. How cool is THAT?

All in all though, I am of the philosophy that you should begin with the end in mind. That said, building a brand is building an asset, and the more distribution channels that asset has available the more valuable it will be in the eyes of future/potential investors.

Is this what freedom from dependence on Amazon feels like?
Is this what freedom from dependence on Amazon feels like?

Now, let’s get into the nitty-gritty.

I’ll start with the obvious first step; sign up for Shopify and get a branded domain ( for example). From here, decisions get a bit more complex. You have to decide to either install a “theme” on your own (this is basically the skin of your website) or hire a site developer.

I’ve personally hired three Shopify site developers in my life and they all ultimately cost about $1000 for a finished site. The benefit to doing it this way is they can set up FBA to Shopify integration for you, so you don’t have to go through any of the manual steps we are about to dive into. You can use a freelancer site (I used Upwork) to find Shopify site developers pretty easily.

If you don’t have the budget for custom work, you can find an inexpensive theme with customizable options and apply the elbow-grease yourself.

After you have a working site, there’s a bit of work involved with FBA integration.

How To Manually Integrate FBA With Shopify

*Please note, this process is only currently available for US and Canada sellers. But don’t worry, if you are in another marketplace, we have a solution further down in this article.

The first step in the process of integration is activating fulfillment by Amazon through MWS. This is a simple process that you will automatically be guided through by visiting

When you’ve gone through the steps to link your Shopify store to MWS, the next step is setting up shipping rates. In your Shipping Settings in Shopify, you need to create “shipping zones” (this just tells Shopify where you ship…such as the United States, Canada, etc).

For each zone, you need to add separate shipping rates. Remember Amazon offers three types of shipping:

  • Standard
  • Expedited
  • Priority

It is advised that you take a look at Amazon’s shipping rates before deciding what you will charge. You can view them here (must be logged into seller central).

Remember to create a separate rate for each shipping option Amazon provides (or that you allow). Remember to use the actual shipping rate name in the Shipping rate name field (Standard, Expedited, Priority). Finally, make sure to set the criteria to Based on order weight (not price).

When this is done, you can configure your product inventory to be tracked by Amazon.

In your Shopify product pages, you’ll see options for “Fulfillment Service” under the Shipping section, and “Inventory Policy” under the Inventory section. Set the Fulfillment Service to Amazon Marketplace Web and Inventory Policy to Amazon Marketplace Web tracks this variant’s inventory, as seen below.

Next, just make sure the Weight and the SKU are EXACTLY the same as they are in Amazon. Then you are good to go!

But here’s where the whole thing gets a little un-fun.

If you rely solely on the Shopify manual integration, you have to also manually send fulfillment orders in….. ☹️

So, whenever you get an order (or whenever you can login to check on things) you need to go to your Orders tab in Shopify, click the order number, and in the Order Details section click Start fulfilling. That brings you to the order’s fulfillment page. Once there, select Mark as fulfilled and then click Fulfill items.

This sends the order to be fulfilled to Amazon. And again, this only works for .com and .ca sellers.

HOWEVER, if you want to automate this process, or if you are in another international market, there is still hope.

Third-Party Shopify Apps To The Rescue

The Shopify app store offers a ton of apps that you can plug into your store that extend functionality. The best part about them is they make complex problems very simple. No coding, no elaborate setup (usually), nothing like that required. Just click-here, click-there, and done.

And there are third-party apps that extend Multi-Channel Fulfillment (what Amazon calls FBA fulfillment of off-Amazon orders) to different marketplaces, different countries and even automates the process.

Now, as I mentioned, I hired developers for my sites, so I haven’t personally used any of the apps that do this, but from my research, I found two. Bytestand, who’s Amazon FBA Shipping app auto-calculates and updates shipping rates as well as automates the fulfillment order process. The major benefit I see to Bytestand is that it also offers this for marketplaces around the world. They also offer a separate app that will import your Amazon listings into Shopify (so you don’t have to copy/paste everything). All that for $25 a month.

Alternatively, Auto Multi-Channel Fulfillment by Webee offers automating MCF orders as well, but also allows for product mapping. This can come in handy if you want to offer bundles and multi-item cart options. This would allow you to bundle items that aren’t currently bundled in the Amazon FBA warehouse. This service is $20 a month. I recommend testing the seven day free trial of both of these, as well as any other Shopify app you may come across.

One More Quick Tip

While the above instructions explain how to set up auto-fulfillment of multi-channel orders through FBA, there is one small setting on the seller central side you may wish to adjust.

Inside of your “Settings” under “Fulfillment by Amazon”…

Fulfillment by Amazon

There are MCF settings that allow you to indicate what information you would like on the packing slip. You may wish to include branded info here.

multi channel fulfillment

Bringing It All Together

Chances are if you are selling private label products on Amazon, you are at least somewhat interested in building a brand. That means the logical next step would be to expand into other distribution channels. Shopify is a great platform that offers near-seamless integration while affording you a branded website. This will ultimately give you access to more marketing channels, more advertising options and ideally more visibility.

But of course, all of this is predicated on getting good products listed on the Amazon platform. And the best way to ensure that is with thorough product research (using tools like Cerebro and Xray), keyword research (using Black Box and Magnet), and an optimized listing (using Scribbles, Frankenstein, and more).

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Anthony Lee Anthony Lee was the training and content manager for Helium 10. An author, consultant and worldwide presenter, Anthony has earned a reputation for rigorous study and data analysis, and how to use that to scale your business in the Amazon seller space.


15 responses to “Marketplace Showdown: Shopify vs Amazon, Which Should You Be Focusing On?”

  1. Hi
    I liked the article that explain everything in step by step…..
    i am interested to set up my Shopify store,but I am not very familiar with the process .
    I have my own website,But I believe you need to have a shopify website?

  2. Great article thanks for the insight. It’s something I’ve experimented with this year, but found that I was spending so much money on Facebook ads without being able to make profit… Most of the time only just breaking even. So I guess with Shopify it’s really just about knowing how to advertise.

    • Just like with any entrepreneurial endeavor, there are many skills involved. Facebook ads is one of them, but I look at them as no different than learning Amazon PPC. I say, either test it out until you figure it out, or hire someone who knows it. 🙂

  3. Thanks for the info! You still have the problem with Amazon MCF shipping your products in Amazon branded boxes right? So if a customer orders from your website, they get your goods in an amazon box and there is a little confusion there.

    I haven’t been able to find a 3rd party warehouse and shipping agent to get anywhere close to amazon’s MCF fees to ship. If Amazon still used plain packaging for their MCF shipments that would be ideal. Any ideas?

    • This is correct. This is a simple and quick solution, but by no means is it a long term one. You’ll need third party fulfillment (or your own warehouse) eventually. I’ve heard good things about Deliverr. Nobody will have the postage rates that Amazon gets, but you save on storage a lot of times (no long term storage fees for example) and sometimes you’ll even save on pick and pack. So, there’s good with the bad.

  4. Hi Anthony,

    I agree that you should do both but definitely get started on Amazon first, there’s a lot more expense and complexity with Shopify selling than with Amazon. Build the base on Amazon so you can finance the Shopify expansion. You can get started pretty cheaply with a free theme, use the free Amazon MCF app for order fulfilment (there is a way to automate the fulfilment so you’re not clicking each order btw), free google shopping app, etc. to keep costs low but it will be difficult to scale your ad spend until you have the site optimized with upsells in place.

    Shopify has way more customer service issues, you’ll also get a lot of scam emails. I prefer than upwork, far quicker and safer although more expensive (they take 15% of the freelancer’s hourly rate and charge a 3% admin fee on the bill). I have found good freelancers on upwork although they were the higher priced ones. There are so many moving parts to entrepreneurship that reducing the headaches and problems is worth the cost imo.

    For order routing go to, insanely powerful rule builder that allows you to integrate all Amazon FBA platforms, a ton of 3rd party fulfilment providers so you can ship internationally, has bundle splitting, item code overrides, updates tracking, allows order splitting if you only have some of your inventory in a particular warehouse (Amazon Australia’s 300 unit storage limit for example). You can also integrate ebay, jet, etc. orders all from the same place if you decide to add those in later.

    For shipping I usually offer free shipping for the Amazon standard shipping, it’s approximately the same fee as what Amazon charges for orders taken on their own platform, good conversion boost and you’re deducting roughly the same shipping cost from your profit as you are on Amazon anyway.

    For google shopping the free Shopify app is a pain, you have very little control over what’s being sent to the google merchant centre. Go to and set the feeds up properly, with all their integrations you’ll likely find more areas to expand into.

    For Shopify themes go to I use their turbo theme, really fast and lots of customizations. They’ve just released a new theme called flex that looks really good as well. They have a 20% discount code. Expensive but cheaper than paying $1000 for a dev. There is a learning curve with doing this yourself but it allows you to make changes and test new things in the future.

    Page load speed is hugely important, especially if you’re running paid traffic. Use a site like to reduce image file size, keep images 1k by 1k pixels, I use Gimp2 for playing around with images. Once you have the site set up how you want, go to and have them optimize the load speeds for your site. They also have a free site analyser designed for ecom. You can also use gtmetrix, webpagetest, google page insights, pingdom. The product pages are where you’ll be sending traffic so they’re the ones to test. I use pagespeedninja for optimizing the code but there are other options.

    One click upsell is great, big fan of it. Make sure you customize the thank you page, add reviews and safe checkout badge to the checkout page, add tracking code in the right places. Be aware that it replaces the shopping cart so you can’t use Shopify payments, you’ll need to set up stripe and paypal for it.

    All of these apps and integrations, along with the freelancers you’ll eventually need, cost monthly fees, relatively cheap on their own but they do add up. With the cost of testing new advertising audiences and creatives on google, facebook, etc. before you find something that works it can add up pretty quickly. Make sure you have the cashflow coming in from Amazon before embarking on it. It takes a lot of time and adds more headache but it does give you more flexibility. The recommendations above are the result of a lot of time and money spent testing loads of other options before finally discovering what works, I wouldn’t want to do this while I was setting up Amazon at the same time.

  5. Hello the Webee site if gone, ? Google it, they have moved, AND the new links are broken too. Perhaps test the link before posting, thanks,

    • If you go to the Shopify app store and search for Auto Multi Channel Fulfillment you’ll see the app by Webee eSolutions.

  6. Hi.My name is Andrew and I am selling private label on Amazon. I just launched my first product last month and just got only 9 sales with 50% coupon during one month . I would like to join with Shopify with FBA . I following the steps you mentioned above but some features didn’t find on Shopify Application . I am using the trial first .


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