minutes = 0
seconds = int(input("How many seconds you want to convert?"))
if seconds >= 60:
We think you've confused two types of statements:
seconds = -60 seconds -= 60
The first one deletes the previous value of seconds and assigns a new value of -60; the second is equivalent to
seconds = seconds - 60
The flow of your code suggests that this second one is what you need; the same change applies to minutes.
You have a conflict in your while logic: although the loop control seems to want to repeat the loop for a while, it gets interrupted during the first iteration by one return statement or the other. You have no way to reach the bottom of the loop and go back for a second iteration.
Why are you returning a Boolean value? That's not clear, since your main code doesn't use it. If you do require the return value, perhaps you need to set a variable within the loop, and then return that variable after the loop.