Hi @Victoria_Ruiz,
That would work — and is probably the best thing to do if you want an ANCOM-style test. Unfortunately, I am not aware of a post-hoc test (e.g., an ANCOM-Tukey test) that is specific to ANCOM that might simplify this process. Check out this forum thread — it sounds like a newer version of ANCOM is available that may support this, and the developers are planning to add that version to QIIME2 in the near future.
You could also check out q2-gneiss. That method is quite useful for working with multivariate datasets, which it sounds like you might be working with, but the downside is that the method can be a bit difficult to interpret if you haven't worked with it before.
I hope that helps!