Though it is feasible of Rhodopseudomonas palustris (R. palustris) stimulation in the cyanobacterial substrate, less is known about its performance under the high ammonium-nitrogen (NH₄-N) circumstance. In the present study, the performance of grown R. palustris Strain PUF1 under an NH₄-N gradient were investigated. Results showed that both the bacterial density and the pigment synthesis were severely inhibited at an NH₄-N concentration of 6.0 g/L, while the ultrathin structure of survived PUF1 wasn’t obviously changed in comparison to NH₄-N concentration ≤3.0 g/L. Noticeably, at an NH₄-N concentration of 3.0 g/L PUF1s recovered its biosynthesis of pigments in a six-day acclimation period. Importantly, the PUF1s thrived in algal substrate under the NH₄-N concentration ≤1.0 g/L with per mL algal substrate 8.96 to 9.88×10⁸ colony formation unit (CFU) on day six. Moreover, it was more diverse of the bacterial consortia in the low NH₄-N treatments (≤1.0 g/L) than that of NH₄-N concentration 3.0-6.0 g/L. Additionally, the excess NH₄-N reduced the sequestration of phosphorus by PUF1s from the algal substrate. Based on the above findings, an NH₄-N threshold up to 1.0 g/L was recommended, it herein produces substantial R. palustris biomass and achieves efficient nutrient sequestration from the protein-rich cyanobacterial feedstock.