What does it mean?

It was a concession, with penalties-not the least of which was, most probably, a dramatically decreased life expectancy

I guess it means you are given a permisson to eat meat, but you could not live longer. What does ‘not the least of which was’ mean?

‘not the least of which was’ means that it was not the least important thing. The author is saying that it was actually a very important thing. In this case, it was a very important ‘penalty’.