Giardia duodenalis is a protozoan parasite of the gastrointestinal tract and the major global contributor to human diarrheal disease. Treatment of Giardiasis is predominately through nitroheterocyclics, specifically metronidazole, which are redox-active compounds believed to induce oxidative damage of DNA and proteins via activation by parasite oxioreductases. However, the effectiveness of metronidazole varies, and resistance is well-documented in both clinical and laboratory settings. Using three isolates of G. duodenalis from the human-infective Assemblage A taxonomic group, we have compared susceptible parent and metronidazole resistant strains of the same isolate using a TMT labelling approach. We identified over 1000 proteins in each isolate, and defined differentially expressed proteins in metronidazole-resistant strains. Though similarities in differential expression between isolates was observed at the level of protein function, there was limited overlap at the protein identification level. This may indicate multiple mechanisms are capable of producing metronidazole resistance in G. duodenalis. We observed differential expression in a wide range of oxidoreductases, some which have been previously implicated in metronidazole resistance and others in FAD and NADH dependent pathways, which are not as well-characterised. These oxidoreductases also showed variable combinations of up- and down-regulation between isolates, further implicating alternate patterns of regulation may achieve similar outcomes for drug resistance. Our results also indicate several post-translational modifications may play a role in resistance, with multiple kinases up-regulated in drug-resistant strains. Furthermore, proteins associated with deacetylase activity were up-regulated, including histone deacetylase and a sirtuin homologue, as well as proteins associated with chromatin remodelling and silencing. This is a novel experimental observation which implicates epigenetic regulation in metronidazole resistance in G. duodenalis.