Pulses are traditionally processed prior to consumption, providing opportunities for modifying nutritional composition, dependant on the type of pulse and method used. In this study, we investigated the effect of whole seed, dehulling (dahl), germination and roasting on changes in mungbean flour nutritional properties, protein composition and relative protein abundance. Processed flours were analysed and compared for protein content, moisture, fat, ash, dietary fibre, total starch and amylose. Significant differences were imparted on dietary fibre content, with roasting and germination increasing the ratio of insoluble/soluble fibre as well as resistant starch. Comparative proteomic analysis resulted in a combined total of 539 protein identifications, searching against the Mungbean reference genome (NCBI Vigna radiata Annotation Release 100). Normalised spectral abundance factors were used as a measure of relative abundance and statistical analysis was applied (Students’ T-Test), where proteins with a p-value of < 0.05 considered significantly different. Processing imparted considerable changes to nutritional composition and should be further exploited for food applications. The comparative proteomic analyses carried out in this study proved useful for investigating the effect of processing on subsequent changes in protein composition and relative abundance.