Hi Stefi, I recommend you check the following:

1- Tannin level is significant; a high level of CT is usually more effective on rumen protozoa; I recommend you check Avila et al. 2020, which could have similar findings.

2- Did you find differences in NH3-N, no effect on NH3-N could explain the lack of impact on Protozoa.

2- Finally, I suggest you track the total bacteria number because, in some cases, especially in short-term studies, the effect of quebracho tannins is much more severe on bacteria, which could unexpectedly and temporarily flourish the protozoal population.

Best of luck my friend

Dear Stefania

The presence of protozoa in the rumen increases the turnover and consumption of nitrogen, so you should consider the NH3-N and microbial protein concentrations.

in another hand, tannins reduce breakdown of protein in the rumen and should reduce the NH3-N concentration

I think you should determine the microbial protein concentration, because the negative relationship between microbial protein concentration and protozoa count, in your case I think the reduction in microbial protein flow to the intestine are normal with case of adding tannins and be logic to increase the protozoa counts