During the culturing of cyanobacteria, heterotrophic bacteria can compete for nutrients, compromise the quality of the harvested biomass, or cause culture crashes. We systematically investigated the effects of depleting inorganic phosphate (Pi) on the growth of the cyanobacterium Synechocystis sp. PCC 6803, its community of heterotrophic bacteria, and the biomass's chemical composition. On the one hand, depleting Pi had minimal impact on total biomass, extracellular polymeric substances (ESP), soluble microbial products (SMP), and most types of intracellular organic polymers production. On the other hand, depleting Pi led to markedly less lipid content, less heterotrophic biomass, and a shift in the heterotrophic community from Burkholderiales to Sphingobacteriales and Saprospirales. The causes of the large impacts were that Synechocystis was much better at scavenging a very low Pi concentration and lowering the Pi available to the heterotrophs. This work lays a foundation for controlling the accumulation of heterotrophs and reducing their deleterious effects in cyanobacteria culturing.