Microbial cluster functions as a key unit in biological wastewater treatment. Mechanistic understanding of early-stage microbial clustering, including kinetics of microbial cluster formation and the driving forces, remains largely unclear. We report an experimental observation of resource availability, in terms of dissolved oxygen, carbon, and nitrogen sources, mediating early-stage formation of microbial clusters. We proposed a simple model for quantifying the role of microbial motility mediated by resources availability in early-stage microbial clustering processes. Simulation results reflected that limited resource availability promotes early-stage microbial cluster formation through enhanced microbial motility essential for sufficient foraging. The results indicate that microorganisms prefer a relative clustering growth pattern to disperse mode in resource-limited environment for survival. It provides new insights on early-stage microbial cluster formation and its dynamics that may improve future design and operations in biological wastewater treatment.