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Currently I have a domain .es for my main store.
Bought my domain for france that ends in .fr
Should I use the .fr domain or create a dubdomain like /fr?
It shouldn’t matter that much, unless you have a physical location for your company/store – and you want Google to suggest it as local business at a specific location.
However, if you’re using a single domain with subdomains (prefixed or as subdirectory), I would suggest you use a more generic domain extensions – .com or something else if not available.
It could be confusing for customers to see the .es extension followed by some other country subdomain.
The most important thing for your SEO is the content itself.