Protic ionic liquids are promising candidates for many applications, including as spacecraft propellants. For both fundamental interest and understanding clustering and dissociation during electrospray‐based propulsion, it is useful to explore the dissociation pathways of protic ionic liquid clusters, as well as the factors affecting the relative contributions of each pathway to the observed MS/MS spectra. With that said, most of the published reports on ionic liquid cluster dissociation have focused on aprotic ionic liquids. The purpose of the current work is to explore the dissociation pathways (eg, loss of amine, nitric acid, or ion pair) of alkylammonium nitrates using energy‐resolved collision‐induced dissociation. Here, it was found that, in general, protic ionic liquids have multiple dissociation pathways—namely, protic ionic liquids can lose their neutralized cation (here, an alkylamine) or neutralized anion (here, nitric acid)—in addition to the ion pair dissociation familiar to aprotic salt and aprotic ionic liquid clusters. In general, increasing the basicity of the cation (here, through increasing the degree of alkylation) decreases the propensity to follow these alternative pathways. Interestingly, increasing the cluster size has a similar effect: as cluster size increases, nitric acid loss decreases. These results will help better model and design protic ionic liquids for electrospray‐based spacecraft propulsion and help provide a better understanding for the general behavior of protic ionic liquids versus aprotic ionic liquids within mass spectrometers.