Hi @MichelaRiba,
There are many forum posts about batch effect and different strategies that have been proposed, so it would be worth searching the forum for similar advice. This discussion also may be relevant:
Based on what you are saying so far, it sounds like decontam (or similar for removing contaminants) might be the best approach for you. I recommend giving that a try.
Carefully reviewing your trimming/truncation/clustering parameters (and quality filtering) would be another good thing to try, though I am guessing from earlier discussion that you are using closed-reference OTU clustering?
A third possibility (if you are comparing to old data) is that there might be methodological variation that you might not be able to control based on this information. E.g., DNA extraction or primer differences?