They still had mouth wash (usually water, vinegar or wine) and they did clean their teeth with linen cloth. And then they'd munch on some good smelling herbs/spices (nutmeg, fennel, etc.) if they could afford it - obviously that was more the purview of the rich but anyone could afford rinsing their mouth with water and giving a vigorous rub. Medieval understanding of healthcare revolved around "bad air" so smelling good was important to them, and of course they tried to keep their mouths and bodies not stanking up and "poisoning" their family and community.

Even cavemen had stonetools and some cavity filling shit they could do for eachother. Only the modern world has people wandering around with shitty teeth and mouths because they can't afford to pay and have shitty diets.