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Ooh, getting complex! "USA is our main market, but it would have the URL .com/us/en/. Do you think that would be a problem" - that should be fine. "We're using /yy/xx/ (country/language), divided in folders. Does it impact SEO? Would you recommend use hyphen instead?" - it's fine the way it is; as long as country is first (so that you can use geo-targeting for each country level folder in Google Search Console) "In this case, if I'm browsing the home page in the USA (.com/us/en/) the canonical would reference the default home (.com)?" - Nope, and be careful here; the canonical tag should reference the correct URL for the current country/language version (in this case, .com/us/en/). You want each country to have/manage its own value. You could attempt to try and do some clever stuff by artificially canonising certain pages to specific countries; however, that'll impact the indexation of those pages in their respective countries, and you'll end up sending people to the wrong versions. "[...] If I visit .com/us/en/ from Australia I stay in the USA version, and get a notification asking me if I want to go to the Australian version. Does it make sense?" - Yup, perfect Your last point on hreflang; it may be that you have some configuration errors, but it may also be that Google believes that for a given query, for a given user, that it's better to serve them the incorrect geographic result (perhaps they're exhibiting strong purchasing behaviour, and the product is unavailable in their territory; or that an unavailable product page is resulting in poor user signals and harming that page's performance)? I'd definitely do some digging into your hreflang configuration to rule that out first, though!

I think I might have found the problem. We're actually, using a 302 redirect from .com to .com/us/en/. From my understanding that doesn't transfer the ranking, right? We use a 302 redirect, because we have multiple stores: https://website.com/us/en/ > United States https://website.com/xl/en/ > Global Store https://website.com.au > Australia If an user visits www.website.com from Australia we send him to https://website.com.au. I'm thinking we should use a redirect 301 to the /us/en/ and keep the 302 for all the other ones. Does it make sense?