Accurately estimating gross primary productivity (GPP) in heterogeneous cropping systems from satellite data poses a challenge. In this study, for the first time, we examined how satellite solar‐induced chlorophyll fluorescence (SIF) tracks GPP in India's diverse cropping system. A significant correlation (r = 0.70–0.90, p ≤ 0.05) at 0.0833° spatial resolution is observed between 8daily and monthly FLUXCOM GPP and Global Ozone Monitoring Experiment‐2 (GOME‐2) SIF. Compared to GOME‐2 SIF the finer resolution, TROPOspheric Monitoring Instrument (TROPOMI) SIF showed greater potential (r = 0.80–0.95, p ≤ 0.05) in estimating GPP and crop productivity, except for Southern and Northeastern parts of India. These regions of India have heterogeneous cropland and low crop area fraction as identified from normalized difference vegetation index (NDVI), near‐infrared reflectance of vegetation and local moran's index map of NDVI. This heterogeneity leads to differences in the timing of growth stages across the annual cycle, such that the SIF signal is characterized by low seasonal variability across the cycle, leading to low correlation between GPP and SIF. Further, in addition to physiological control the intra‐annual variability of GPP‐SIF relationship (GPP/SIF ratio) is influenced by temperature, radiation, and moisture availability during peak/late growing seasons. However, in the early growing season, it primarily relies on soil moisture. Our findings should help improve GPP estimation using SIF across the agricultural ecosystems of India.