Yield and protein recovery are important variables for process design, which cannot be achieved using degree of hydrolysis (DH). Even though it is known that mixing speed and solids concentration affect mass and energy transfer in bioprocess reaction, previous research has not provided a clear relationship between these two variables and their effect on yield of dry solids and protein recovery during enzyme hydrolysis. The yield of dry solids and protein recovery from enzyme hydrolysis of sardine processing by-products was compared at different levels of mixing speed (100–300 rpm), solids concentration (26–50%) and enzyme dosage (1.318–4.682%). Results showed that low mixing speed (100 rpm), low solids concentration (26–30.8%) and high enzyme dosage (4.682%) optimised degree of hydrolysis to 25.7%, yield of dry solids to 69.1% and protein recovery to 83.0%. Under these conditions, protein loss to emulsion and sludge were minimised to 5.82% and 11.2%, respectively. Although low solids concentration resulted in high solids yield and high protein recovery due to favourable mass transfer effects, hydrolysing material under these conditions will come at a significant cost of larger equipment designs and energy cost for mixing and downstream processing because of the large volume of water to be handled. There is therefore a need for a holistic approach to enzyme hydrolysis optimisation studies, with downstream processing in mind. The significant findings of this study show the impact of process variables and their interaction, particularly solids concentration, on process performance using multivariable optimisation.