Intracellular pathogens frequently subjugate the ubiquitin system to evade host immune defenses and establish intracellular replication niches. Microsporidia are obligate intracellular animal parasites that typically cause self-limiting infections in humans, but can sometimes cause fatal disseminated disease. At present, the ubiquitin system of microsporidia is virtually unexplored. Here, we discover a likely effector deubiquitinase (DUB) of the otubain subgroup from the human pathogenic microsporidian , which we designate ehOTUB1. We find that ehOTUB1 selectively binds the human ubiquitin conjugating (E2) enzyme UBE2K and inhibits its ubiquitin conjugation activity independent of ehOTUB1 DUB activity. We show that ehOTUB1 obstructs docking of UBE2K onto ubiquitin E1 enzyme via steric conflict with ubiquitin in the E1 adenylation site to prevent ubiquitin transfer to UBE2K. This unconventional mechanism of E2 inhibition expands the known repertoire by which pathogens manipulate ubiquitin signaling, and suggests that direct inhibition of E2 enzymes may be a broader function of otubain subfamily DUBs than originally appreciated.