Food to microorganisms ratio (F/M) and sludge retention time (SRT) are known to affect in different ways biomass growth, bioactivities and foulants characteristics. Thus the aim of this study was to dissociate the effects of SRT from those of F/M ratio on lab-scale membrane bioreactors performances during stable and unstable state. Two acclimations were stabilized at a SRT of either 20 or 50 d with a constant F/M ratio of 0.2 kgCOD kgMLVSS−1 d−1. During stable state, a higher N-NH4+ removal rate (78%) was obtained at SRT of 50 d as an easier autotroph development was observed. Soluble microbial products (SMPs) release was double at 50 d with a majority of polysaccharides (49% of total SMP). The unstable conditions consisted in F/M ratio changes and operation without air and nutrient. Autotrophs were highly affected by the tested disturbances and SMP retention on membrane surface exhibited consistent changes during the performed stresses.