My boyfriend and i tested positive on chlamydia. we both took the medication but had sex two days after. did the infection most likely stay?

Maybe: The fact that you both took the medicine is a good sign. Theoretically, it should be the same "strain" of chlamydia if you two are only having intercourse with each other, but it had to come from somewhere. Either one or both of you had it prior to your first sexual encounter. It raises the question of whether or not one or both of you have been sleeping with others. Further STD test is needed