Bromelain, a set of proteolytic enzymes potential pharmaceutical applications, was encapsulated in chitosan nanoparticles to enhance enzyme stability, and the effect of different chitosan sources was evaluated. Chitosan types (i.e., low molecular weight chitosan, chitosan oligosaccharide lactate, and chitosan from shrimp shells) produced nanoparticles with different physicochemical properties, however in all cases, particle size and zeta potential decreased, and polydispersity index increased after bromelain addition. Bromelain encapsulation was higher than 84% and 79% for protein content and enzymatic activity, respectively, with low molecular weight chitosan presenting the highest encapsulation efficiency. Nanoparticle suspension was also tested for accelerated stability and rheological behavior. For the chitosan–bromelain nanoparticles, an instability index below 0.3 was recorded and, in general, the loading of bromelain in chitosan nanoparticles decreased the cohesiveness of the final suspension.