Current pelvic inflammatory disease (PID) treatment effectively treats Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT). However, coverage may be inadequate for Mycoplasma genitalium (MG)/Trichomonas vaginalis (TV) infections. We compared the longitudinal MG and TV outcomes with NG/CT outcomes for women enrolled in a longitudinal randomized controlled trial to optimize outcomes after PID. The prevalences of CT and NG were lower at 30- and 90-day follow-up compared with the prevalence at the time of diagnosis. No significant difference was observed for MG (odds ratio, 0.95; 0.86–1.04; P = 0.265) and TV (odds ratio, 0.89; 0.75–1.04; P = 0.146) over time for both treatment groups, showing that persistence and/or reinfection with MG and TV occurs more frequently than with CT or NG after treatment of PID using current national treatment guidelines.