Receptors to be downregulated via the lysosomal degradation pathway are retained at the endosomal membrane through ubiquitination, where invagination of the endosomal membrane incorporates receptors into intralumenal vesicles (ILVs) and commits them for degradation. AMSH (Associated Molecule of the SH3 domain of STAM), an auxiliary protein of the ESCRT machinery, contains a C-terminal JAMM metalloprotease domain that hydrolyses K-63 linked ubiquitin chains in vitro, leading to the hypothesis AMSH functions to remove ubiquitin from receptors before their incorporation into ILVs. AMSH also interacts with CHMP proteins of ESCRT-III through a predicted MIT domain-containing N-terminal domain. Binding to a CHMP C-terminal auto-inhibitory domain has implicated AMSH in the activation of CHMP proteins for polymerisation to effectuate membrane remodelling. This work shows AMSH can bind to two distinct forms of CHMP3; an open, activated form, and a closed, auto-inhibited form. The interaction of the AMSH N-terminal domain with both CHMP3 forms has been measured by isothermal titration calorimetry to be of nanomolar affinity, with the last 40 amino acids of the CHMP3 C-terminal required for maximum affinity. The x-ray crystallographic structure of an AMSH N-terminal-CHMP3 complex has been determined to 1.7Å resolution, presenting a mode of CHMP3 binding distinct from previously characterised MIT-CHMP structures and a deviation from the classical MIT domain architecture. We provide evidence that the N-terminal domain of AMSH interacts intramolecularly with the enzymatic JAMM domain, and that this interaction stimulates the deubiquitinating activity of the JAMM domain. These results highlight a particularly high affinity binding between AMSH and CHMP3, wherethe dynamics of CHMP binding and the efficient deubiquitinating activity of AMSH can create a point of regulation in the endosomal sorting pathway.