A key step in the production of polyhydroxyalkanoates (PHAs) from organic waste streams is the selection of a biomass with a high PHA-storage capacity (selection-step), which is usually performed in sequencing batch reactor (SBR) according to the state-of-the-art. A major step forward would however to be able to perform such selection in continuous reactors, which would broaden opportunities for a full-scale implementation PHA production using municipal wastewater (MWW)-derived feedstock. The present study therefore investigates to what extent a simple continuous-flow stirred-tank reactor (CSTR) represents a relevant alternative to an aerobic feast-famine SBR for the selection of PHA-storing biomass. To this end, we operated two selection reactors (CSTR vs. SBR) on filtered primary sludge fermentate while performing a detailed analysis of the microbial communities and monitoring PHA-storage over long-term (~150 days) and during accumulation batches. Our study demonstrates that a simple CSTR is as effective as an SBR in selecting biomass with high PHA-storage capacity (up to 0.65 gPHA gVSS-1) while being 50% more efficient in terms of substrate to biomass conversion yields. We also demonstrated that such selection occurs in excess of nitrogen (N) and phosphorus (P), whereas previously P limitation was the only known factor giving a competitive advantage to PHA-storing organisms in a single CSTR. We further found that the microbial community compositions are mostly affected by the nutrient availability rather than by the reactor operation mode (CSTR vs. SBR). Similar microbial communities therefore developed in both selection reactors, while microbial communities were very different depending on N availability. Rhodobacteraceae gen. were most abundant when growth conditions were stable and N-limited, whereas dynamic N- (and P-)excess conditions favoured the selection of the known PHA-storer Comamonas, and led to the highest observed PHA-storage capacity. Overall, we demonstrate that biomass with high storage capacity can be selected in a simple CSTR on a wider range of feedstock than only P-limited ones.