Very recently, a new class of cosolvents, hybrid ionic fluids (HIFs), have been designed by combining an ionic liquid (IL) and a deep eutectic solvent (DES) with a common anion. The product HIF formed is devoid of the deleterious effects of one component and has augmented advantageous characteristics of the other component, and is emerging as a fascinating sustainable solvent media and a new environmentally friendly solvent for biomolecules. Herein, we present the effects of 1-ethyl-3methylimidazolium chloride ([Emim][Cl]), DES (synthesized using 1:2 choline chloride and glycerol), and their respective HIF on the structural stability and enzymatic activity of stem bromelain (SB). The spectroscopic results explicitly elucidated that [Emim][Cl] interacts favorably with SB and affects the structural as well as thermal stability of SB, whereas the stability and activity of the enzyme were increased in DES. Interestingly, the results obtained for HIF were the intermediate of the two (IL and DES) as the enzymatic activity of SB in the presence of HIF is maintained at all studied concentrations. Moreover, with the help of TEM and AFM studies, the changes in morphologies of SB in the presence and in the absence of IL, DES, and HIF were ascertained, and it was found that the morphology of SB in the presence of HIF and DES was similar to that of SB in buffer (control), indicating that DES and HIF preserve the native structure of SB. In other words, the morphology of SB has changed in the presence of IL. Apparently, the morphological results are in accordance with the spectroscopic results; thus, HIF significantly enhances the structural stability and enzymatic activity of SB, eventually confirming the suitability of HIF media as a potential and ecofriendly prolonged storage system for SB's native structure.