It is possible to create different tax settings for different collections of products. If you read the dialogue I had in this thread the solution is there. When you have multiple product types you have to get creative with the combinations Shopify offers. Including discount codes for certain regions only etc.
Thanks for your reply! I did indeed use the solutions in this thread to
apply different taxes to charge only one tax on some of my products.
My issue now is that there’s no way to alter the taxes charged on shipping,
not just products. It may seem like a minor quibble but it’s an unnecessary
charge that the customer shouldn’t have to cover. But it seems as though
it’s “just the way it is” so I’ll stop complaining about it now. 
Thanks to everyone for their insights.
I’m having the same issues for my own Shopify bookstore, but one thing I thought of could be to just provide a refund to the customer for the amount that they were overcharged for the taxes on shipping. Admittedly, It would be a little tedious to have to do this for each and every order, but it might be a simpler solution than tracking the overcharged amount and then remitting to the appropriate province? Curious to get other people’s thoughts on this as well!
Hi @DF88 ,
Certainly you could do a refund for every transaction for the provincial sales tax portion on every order. And since you are a bookstore, I’d say you probably should. Our store sells a wide variety of items, and books form only a small portion.
I have to track every order and break out the taxes of each, regardless if the tax is or is not charged. I do an excel spreadsheet for every payout, breaking down each transaction. Then I use the totals from it to input to my accounting software, so it can be captured and tallied for when I do remittances. Sure, I could input each transaction into the software directly, but I think it is easier to find errors and handle it with a spreadsheet first.
This is clearly a Bug, but Shopify support does not acknowledge it.
I spent 2 hours explaining & waiting with Shopify Live Chat Support. This is the response I got: “You have successfully created the Tax Override, however it’s “null” do to incoherent Tax Rates that don’t work together appropriately.” – meaning – Selling multiple categories in a Shopify website is simply not possible, because each category carries a different tax. (If manual collection override option worked, this wouldn’t be a problem)
I sell multiple types of items in my store, and for the books/magazines that require a different tax I use the manual collection method and it works. Customers can order a book and be charged one tax rate and order another item and be charged the correct tax rate for it. Try looking back to earlier posts in this thread and see if that helps.
Also, you can not override shipping to match the tax rate if a customer only orders books. (discussed above).
@NoName30 this worked! Thanks so much. I took a screen cap and filed it away for later, in case Shopify wipes my settings like you mentioned
Yeah!! Glad it could help you. 
Thanks for your help with this. I’m having the same issue, but I don’t see the option to set tax rates by province. Is there something obvious I’m missing?
Go to Settings, Taxes and Duties, Click on Canada. In the Sales Tax Collection Box you click “Collect Sales Tax”. Then select region and you’ll put in your sales tax id for that region if you haven’t already set them up.
Then you go the Product Overrides Box (still under Canada) and click “Add Product Override”. Then proceed per my post of Jan. 16, 2021 above. You’ll need to have first made a manual collection for the books in order to do the product override.
Thanks for your reply! However, when I enter my sales tax ID for any region under GST/HST, it says, “Adding GST to [province] will apply GST to all Canada and HST to participating provinces. This is because GST/HST is the same tax account.” Then when I add it, it says “You’re collecting sales tax in Canada,” and no longer allows me to set up those individual tax rates by region. (And when I do a tax override for Canada, it doesn’t seem to do anything–I tried using both 5% and 0%). I’ve contacted Shopify Support, but they haven’t figured it out yet either…
First of all, have you set up a manual collection for your books (Products, Collections, Create Collection, Select Manual Collection Type)? You cannot have the sales tax changed for an automated collection.
Yes I did. I can assign the tax to that manual collection for Canada (only), but it makes no difference to what is being charged.
Actually, I tried adding a tax rate for individual provinces and it works now! I think the issue was I had originally just set to collect tax for Canada, and when I checked now, was able to set for individual provinces. Thanks so much!
I’m curious why the rate is 5% for Quebec, when it doesn’t charge HST. Seems for all the other provinces that don’t charge HST/charge PST+GST instead, the rate is 0%.
This is a very thorough response. I’m having a similar issue with children’s clothing. In Ontario, it is only charge the federal 5% and not the 8% provincial. I’m going to give this a whirl! I’ll update if it works for me too.
Unfortunately, no luck for me.
Have you created a Manual collection for overriding the PST tax on children’s clothing? You need to do this; it can’t be done with an automated collection. You go to Products, Collections, Create Collection.
Then you add all the children’s clothing to this manual collection. Each child’s clothing that is PST exempt will still also be in the automated collection as well as in the Manual collection.
Presuming you’ve already set up your GST/HST tax number in the taxes, you will then you create a product override under Settings, Taxes and Duties, Regional Tax Settings - select Canada, Product Override +Override, put in the name of the Manual Collection you made, select Ontario in the pull-down menu, and put in 5% for the tax.
Thank you! I did the original manual collection for the PST but I somehow missed the step adding the 2nd manual collection. Thank you so much it worked perfectly.