Both routes create a legal corporation. The difference shows up later, in where you can operate and what you're required to file.
Incorporating federally versus provincially both result in a legal corporation with the same basic protections — namely, separating the business's liabilities from your personal assets. The choice between them matters less for what it does on day one and more for how the business is likely to operate down the road.
The practical difference
A provincial incorporation registers your business in one province, with name protection limited to that province. If you plan to operate mainly in one place and don't expect to expand across provincial lines any time soon, it's typically simpler and less expensive to set up and maintain. A federal incorporation gives you name protection and the right to operate across Canada, which matters if you're already planning to expand into other provinces or want the stronger name protection regardless of near-term plans.
One thing that surprises a lot of new owners: a federal incorporation still requires registering as an extra-provincial corporation in each province where you actually do business, on top of the federal filing. It's not a single filing that eliminates provincial paperwork entirely — it adds a layer rather than replacing one.
What actually drives the decision
For most single-location small businesses with no near-term plans to expand provinces, provincial incorporation is the more common and more cost-effective choice. If your business name matters a lot to your brand and you want it protected nationally, or you already know you'll be operating in more than one province within a year or two, federal incorporation is worth the extra setup cost.