While poking around Google's new Search Console I ran into this little option in the URL inspector.
Notice the last item there, "Google-selected canonical" which is the inspected URL. I also popped up the help text for you too.
The url I tested was the product-only url, one that looks like /products/product-handle
Compare that to what Google shows for the same product but within a collection, what Shopify calls a collection-aware link.
Notice how the Google-selected canonical is different: "Same as user-declared canonical". Also notice how right above that the user-declared canonical isn't the page I'm inspecting, but rather the product-only url from before.
This tells me that Google is ignoring the collection version in favor of the product-only url. Exactly what you want and what Shopify tries to do for you.
This simple addition to Search Console is going to make it easier to troubleshoot the really sticky problems with canonicalization.
In a similar thread, a lot of people has been asking for advice on the collection url problems in Shopify. This new feature of Search Console will make it easier to illustrate it for you, while also letting you test your own store.
I'll probably have that article and advice ready in the next few months. Though at this time I'd recommend waiting to apply it until after the holidays. It could cause a large disturbance in the force, enough to screw with your SEO traffic. It's too risky to apply right now. At least without someone well-versed in SEO who is able to guide you through the entire process (e.g. not me).
There's something else you can do now with much less risk to your SEO.
Google has been working on Rich Results a lot this year which means the stores that provide the correct structured data are getting a leg up on their competitors.
And JSON-LD for SEO is the easiest and safest option in the Shopify app store to automatically add that data.
Already trusted by thousands of Shopify stores, it's among the top SEO apps overall.
Eric Davis