An experiment consisting of nine treatments was conducted at Main Agricultural Research Station, Dharwad during kharif season of 2014-2015 to evaluate the Influence of site specific nutrient management and target yield on expression of Cry protein, quality parameters and pest population in Bt-cotton (Gossypium hirsutum) under rainfed condition. Studies indicated that, application of nutrients for the target yield of 45 q ha-1 (241.7:63.4:259.5 kg N: P2O5: K2O ha-1) recorded significantly higher Cry 1Ac and cry 2Ab (5.30, 0.88, and 20.51, 16.72, µg g-1 fresh weight at 60 and 120 DAS respectively), sucking pests (jassids, aphids, thrips, mites, white flies and mirid bugs) and midges population compared to other levels of nutrients applied based on target yield. NDVI and SPAD chlorophyll readings followed same pattern as that of Cry protein expression and pest population. There was no significant difference with respect to fibre length, fibre strength, uniformity ratio, maturity ratio, fibre elongation, ginning out turn and micronaire value among the different nutrient levels through target yield approach. The study also revealed that among the different target yields, 45 q ha-1 target yield recorded significantly higher seed cotton yield (39.13 q ha-1) over other target yields. However, 35 and 40 q ha-1 target yield level were on par with target yield level of 45 q ha-1.