The aim of this paper, in which clogging occurs on the filter at a constant vacuum pressure and constant pectin weight, is to find the optimal values of the variables, temperature and time, to know the best conditions to reduce this clogging by enzymatic hydrolysis. Moreover, different properties of the compression of the cake in the filter were determined such as the filtering medium total resistance (RfT), bed porosity (ε) and the cake-specific resistance (α) at different times and temperatures. The filter area was 0.142 m2, and the value of the mass fraction of solids in the filtered suspension (S) was 0.12. Scanning electron microsopy (SEM) analyses were performed. The results showed that the compressive stress corresponding to the cake improves the flow rate in the filtration flux at the optimal temperature and time for the process, where the enzyme reaches its highest activity. The test results of this study can be applied in different system of filters during cross-flow filtration.