In this study, the flux decline mechanisms were identified during membrane clarification of red plum juice at several processing parameters, including pore size, membrane type, transmembrane pressure, temperature and velocity. The results were used to investigate the effect of changes in operating conditions on the intensity of membrane fouling. Also, scanning electron microscopy (SEM) was used for analysing fouling-layer morphology. These results showed that the main mechanism responsible for membrane fouling was cake formation (over 95% fitness) occurring in the first stage of the process. Intermediate, standard and complete blockings were formed during most of the runs as filtration proceeded. The results also indicated that increasing the temperature from 30 to 40 °C was the most effective factor in decreasing cake-layer fouling, reducing it by about 66.7%. Furthermore, an increase in processing velocity of up to 0.5 m s−1 had the greatest effect on intermediate blocking, reducing it by about 86.1%. Also, increasing pressure up to 2.9 bar completely eliminated standard blocking and complete blocking. Finally, microstructure analysis of membrane using SEM confirmed that cake formation had the greatest impact on membrane fouling.