I was prescribed 500mg of amoxicillin twice a day for an ear infection. three days after starting the medication, i took a urine based naa test for chlamydia and gonorrhea, result was negative. could the amoxi have caused a false negative that soon?

Yes, amoxicillin could work that fast to make a test negative, but usually by curing the infection, not just suppressing it. (Amoxicillin isn't routinely recommended for either gonorrhea or chlamydia, but usually would cure either one.) You could consider another test 1-2 weeks after completing the amoxicillin, but it really isn't necessary unless you need the reassurance.