Polyphosphate-accumulating organisms (PAOs) play a crucial role in enhanced biological phosphorus removal (EBPR) processes. In addition to biosynthesis, they rely on phosphate for energy generation. However,
Candidatus
Accumulibacter, a model PAO, has been shown to adapt to low phosphate conditions by switching to a glycogen-accumulating metabolism (GAM), with variable success across genus members and experiments. This study aimed to explore the metabolic shift of several
Accumulibacter
species subjected to low-phosphate concentration in different operating conditions using metatranscriptomics analysis. Furthermore, the study enabled a comparison of the transcriptomic profiles of
Accumulibacter
with those of
Propionivibrio
, a glycogen-accumulating organism typically found in EBPR plants. Two sequencing batch reactors were operated with different carbon sources to enrich for different populations of
Accumulibacter
. After decreasing the influent phosphate concentration, carbon removal performance was maintained while anaerobic phosphate release dropped dramatically, suggesting a shift from a phosphate-accumulating to a glycogen-accumulating metabolism. Analysis of metatranscriptomics data indicated that
Accumulibacter regalis
(type I) and
Propionivibrio aalborgensis
remained the most abundant species after the phosphate decrease in the reactor with acetate-propionate and allylthiourea, while
Accumulibacter delftensis
(type I) and
Accumulibacter phosphatis
(type II) remained active in the reactor with acetate-glucose and no allylthiourea. Transcription of the genes from the ethylmalonyl-CoA pathway involved in the production of propionyl-CoA and regulation of the anaerobic redox balance was enhanced under low-phosphate conditions, especially for type I
Accumulibacter
. Conversely, the transcription of the methylmalonyl-CoA pathway was enhanced under low-phosphate conditions in
Propionivibrio
and type II
Accumulibacter
.