Field experiments were conducted to standardize protocols for site-specific fertilizer nitrogen (N) management in Bt cotton using Soil Plant Analysis Development (SPAD) chlorophyll meter. Performance of different SPAD-based site-specific N management scenarios was evaluated vis-à-vis blanket fertilizer N recommendation. The N treatments comprised a no-N (control), four fixed-time and fixed N doses (60, 90, 120, and 150 kg N ha-1) including the recommended dose (150 kg ha-1), and eight fixed-time and adjustable N doses based on critical SPAD readings of 45 and 41 at first flowering and boll formation stages, respectively. The results revealed that by applying 45 or 60 kg N ha-1 at thinning stage of the crop and critical SPAD value-guided dose of 45 or 30 kg N ha-1 at first flowering stage resulted in yields similar to that recorded by applying the recommended dose of 150 kg N ha-1. However, significantly higher N use efficiency as well as 30–40% less total fertilizer N use was recorded with site-specific N management. Applying 30 kg N ha-1 at thinning and SPAD meter-guided 45 kg N ha-1 at first flowering were not enough and required additional SPAD meter-guided 45 kg N ha-1 at boll formation for sustaining yield levels equivalent to those observed by following blanket recommendation but resulted in 20% less fertilizer N application. Our data revealed that SPAD meter-based site-specific N management in Bt cotton results in optimum yield with dynamic adjustment of fertilizer N doses at first flowering and boll formation stages. The total amount of N fertilizer following site-specific management strategies was substantially less than the blanket recommendation of 150 kg N ha-1, but the extent may vary in different fields.