Soil test based fertilizer prescription equations (FPEs) were developed for desired yield target of transgenic cotton under Integrated Plant Nutrition System (IPNS) through drip fertigation on Vertic Ustropept of Tamil Nadu, south India. To validate the equations, an experiment was conducted on the same soil series. The results revealed that the deviation recorded in the achievement of target aimed, was within the range of ±10% (90–110%) proving the validity of the FPEs. STCR treatments greatly influenced the growth and yield attributes of the crop and recorded significantly higher yield, response ratio (RR) and benefit-cost ratio (BCR) than blanket, farmer's practice and control. STCR-IPNS treatments performed better than STCR-NPK alone treatments. There was build-up of post-harvest soil fertility in the STCR treatments. The treatment, STCR-IPNS for 4.0 t/ha of cotton proved its superiority over all other treatments in terms of yield, uptake, response ratio, BCR and quality parameters. This treatment recorded an yield increase of 62.4 and 65.6%, respectively, over blanket and farmer's practice. Therefore, it could be concluded that these FPEs could be made use of for prescribing soil test based fertilizer doses for transgenic cotton on Inceptisols under drip fertigation.