Fertilization of Nitrogen (N), phosphorus (P) and potassium (K) is an effective strategy for improving tea yield and quality. Even though, NPK fertilization enhances tea yield and quality, addressing soil deficiencies to boost growth, but also impacts soil microbes, influencing nutrient cycling and yield. Therefore, the objective of this study was to assess the effect of different NPK fertilizer application rates on microbial composition of J. zeyheri tea under greenhouse conditions. Six treatments constituting NPK fertilizer rates (2:3:2 ratio) @ 0, 2, 4, 8, 16 and 32 g were arranged in a randomized complete block design, with five replications. 130 days after initiating treatments, leaves were harvested and oven-dried for 72 h at a temperature of 60°C. After laboratory preparations, microorganisms on tea leaves were determined by the principle most probable number using the Tempo reader (BioMerieux, Rodolphe, Durham, United States) instrument. Treatments had a highly significant effect (P ≤ 0.01) on Bacillus cereus contributing 39% in total treatment variation (TTV), whereas increasing NPK fertilizer rates had significant effects (P ≤ 0.05) on Enterobacteriaceae contributing 58% in TTV. Increasing rates of NPK fertilizer did not influence total coliforms contained in J. zeyheri tea leaf tissues. Bacillus cereus and Enterobacteriaceae over increasing NPK fertilizer rates exhibited positive quadratic relations, with density dependent growth pattern. Fertilizer requirements for Bacillus cereus and Enterobacteriaceae under greenhouse conditions were optimized at 1.75 g fertilizer/plant. In conclusion, Bacillus cereus and Enterobacteriaceae were affected by increasing NPK fertilizer rates.