Microencapsulation can improve the viability of probiotic cells during storage and digestion. In this study, a double emulsion microencapsulation system WC/O/WF was designed to microencapsulate Lactobacillus rhamnosus GG using pea protein (PP) and cellulose nanocrystals (CNC). The double emulsions were prepared by a two-step emulsification process. Six formulations of WF were tested with varying proportions of PP:CNC. Double emulsions with higher CNC proportions were significantly more stable and showed smaller particle sizes. The encapsulation efficiency for all the emulsions did not differ significantly. The double emulsions significantly improved the viability of encapsulated cells during a simulated gastrointestinal digestion study. CNC delayed the digestion of PP in the gastric phase but did not affect the overall degree of hydrolysis. The study presented promising results for employing a double emulsion system for the microencapsulation of probiotics and the potential of PP and CNC in designing such systems.