As all ways, depends on the time, place, customs and who is writing about the people in question. The Medieval era covers a period three times longer than the Early Modern era, which itself is almost unrecognizable from Columbus to Napoleon.
Certain places would definitely have been much "filthier" than others. Lime was not ubiquitious everywhere, modern global trade was not the common thing, and a village would generally only have strong access to local goods. People in Paris in 1400 may actually have been filthy compared to a rural serf under great strife in late 700s Viking Normandy because they had access to clean, fresh water and weren't surrounded by disgusting people expelling effluent on the roads. Anyone able to keep up with Islamic hygiene rules would certainly have been far cleaner than anyone else as they ritually wash after seeing a poor person cross the road. At the same time, a Cypriot would be disgusted by the idea that you wipe with your hand (then wash the hand) rather than use a briny sponge.
At the same time, it is far easier to be clean to the point you die of seasonal diseases today than ever before, yet we still have people walking around in public without shame looking like someone from Monty Python. Most of the "the Dark Ages were filthy" ideas come from the Enlightenment, both terms being used to point out what the Early Modern writers believed to a hole of progress after the collapse of the Roman Empire. In a sense, they were right. Aquaducts, public toilets, and (in places that could have them) public baths/saunas crumbled in many places because they were capital intensive. The "regression" to Feudal and tribal organisation of society meant they couldn't be maintained properly. Anyone who lived in a city with maintained Thermae or Balnae like modern Aix-le-Bains or Bath would be unlikely to have noticed much of a difference between 50 AD and 1550 AD, but someone living in what was a relative back water like Londinium would have noticed a huge difference as bathing in the river became increasingly impossible and not solved until well into the late 1800s. The cast of Monty Python were also traveling a lot- it doesn't make that much sense for everyone at Swamp Castle to be filthy during a Baronial celebration, but it makes sense for the Anarchist Communites to be while digging their mud. There are also few opportunities to wash during a siege, where water is rationed.
