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What preposition should I use before 'molecular level'?

I'm going to make an example, which I totally made up, just for clarity.

The presence of this organism within the liver causes changes on/at (a) molecular level.

What I mean is that these changes will occur because of their influence on the liver's molecules.

I ran a search on ngram, and 'on a' seems to be the winner, but not by much, so I would like to hear someone else's opinion.

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Both "at a level" and "on a level" are used in different contexts. For any given context, such as your specific example, there may be one that has become more idiomatic through use, or there may be a logical reason why one is correct.

Generally speaking, "at" means that you have reached something, but are not necessarily in it, or on it. For example - if you were in an elevator and you reached the 4th floor, you might say "I'm at the 4th floor". However, once you stepped out of the elevator and onto the floor you might say "I'm on the 4th floor".

Saying something is operating "at a level" suggests that they are parallel with it. But saying that something is operating "on a level" suggests some involvement or interactivity with other things that are also on that level.

I'm no expert in the field that you're speaking about, but I would guess that "operating on a molecular level" means that something is actually interacting with molecules, which would explain why "on" is the idiomatic preposition.

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