Protein unfolding is the main emulsifying mechanism in meat products. However, myofibrillar protein depletion resulting from endogenous or exogenous protease activity affects the emulsifying properties. The objective of this work was to study the effect of endogenous and exogenous proteases on protein depletion, emulsifying and viscosity properties in a model meat emulsion. Pork and shark meat were treated with a Pseudomonas fluorescens protease extract; endogenous proteolytic activity was studied in non-treated meat; samples were stored at 4 and 15 °C up to 15 days and emulsions formulated with extracted myofibrillar proteins. Endogenous proteolytic activity of shark meat extracts was significantly higher as compared to pork, promoting more extended protein degradation. This resulted in lower viscosity of protein extracts and emulsions. However, viscosity increased in both species throughout the study time, probably due to protein unfolding and molecular interaction. Emulsion capacity and stability increased in pork but decreased in shark, due to exogenous protease addition.