It's possible that you might be able to submit the Farmer Quota certificates during TS EAMCET counselling, but there is no guarantee.

The official brochure or website of TS EAMCET counselling typically outlines the documents required during registration and the window for submitting them. These documents usually include certificates for claiming reservation benefits like the Farmer Quota.

Some counselling processes might have a separate window for submitting certificates for claiming reservation benefits like the Farmer Quota. This window could be after the initial registration but before the final seat allotment.There is also a chance that the counselling process might not allow submission of such certificates after the initial registration deadline.

https://engineering.careers360.com/download/ebooks/ts-eamcet-preparation-tips

I hope it helps!