The study addresses the challenge of intensifying biological wastewater treatment by regulating the metabolic activity of activated sludge. Insufficient stability in treatment plant performance, often caused by sludge bulking and poor sedimentation, necessitates innovative methods for microbiocenosis management. An ecobiotechnological approach was developed using tricarboxylic acid (TCA) cycle metabolites, specifically citrate and succinate, as biostimulation factors in ultra-low concentrations (0.1–10 mM). The study also examined the combined effect of these metabolites with malonate, a competitive inhibitor, on the Sludge Volume Index (SVI) and species diversity. For the first time, it was established that ultra-low concentrations of TCA metabolites effectively activate decomposer metabolism without disrupting cellular ionic balance. Citrate treatment led to a qualitative transformation of microbiocenosis, increasing the abundance of free-swimming ciliates 3.1-fold, attached ciliates 2.6-fold, and Zoogloea ramigera bacteria 1.8-fold. A significant novel finding is the 5-fold suppression of filamentous sulfur bacteria by citrate, which prevents sludge bulking. Succinate was found to stimulate higher trophic levels (Rotifera, Tardigrada), enhancing wastewater clarification through increased species diversity. Furthermore, the combined application of citrate, succinate, and malonate stabilized the population of each species within the biocenosis, successfully reducing the SVI from 235 to 195. The proposed activation technique ensures the sustainable development of modern wastewater systems by providing a controlled mechanism to improve sedimentation properties and treatment efficiency through metabolic regulation.