Trichomonas vaginalis, an extracellular, flagellated protozoan parasite, is the etiologic agent for trichomoniasis, the most common non-viral sexually transmitted infection, trichomoniasis. While asymptomatic presentation is commonplace, symptomatic infections typically present as vaginitis and cervicitis in women, and urethritis in men. Only 5-nitroimidazole class of drugs, metronidazole (Mz) and tinidazole, is FDA-approved for treatment of infections. To overcome the knowledge gap in Mz targets in T. vaginalis, we used metronidazole-alkyne analog and we employed copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) “click” reaction to enrich these protein targets. Using tandem mass tag quantitative proteomics, we identified novel protein targets in Mz-sensitive and -resistant parasites. We also determined through activity-based protein profiling that metronidazole binds to cysteine residues and subsequently identified cysteine residues that are bound by metronidazole. As the nature of immune response to T. vaginalis infection appears to vary, we also explored whether T. vaginalis parasites harboring M. hominis, an endosymbiont, induce the production of different cytokines from primary human monocytes compared to parasites that do not harbor the endosymbiont. Indeed, we observe that more cytokines are elaborated in response to M. hominis infected parasites. Together, these studies illuminate our knowledge of this important human pathogen, pharmacologically and immunologically.