<p>This study presents a comprehensive analysis of the influence of ENSO events on soil moisture, rainfall, and soybean crop yields, alongside an evaluation of trends and their correlations with soybean crop yield. GLDAS soil moisture data were retrieved, pre-processed, and agriculturally masked using Google Earth Engine (GEE), while IMD rainfall data were processed locally and integrated for zonal statistics in Marathwada and Vidarbha. Trends for 2003–2022 were assessed using the Mann-Kendall test. Marathwada and Vidarbha regions, contributing 39% of India’s soybean production, were found to be highly susceptible to El Niño events especially western and central parts of this region. El Niño negatively affected crop yield, with reductions ranging from − 12 to -70%, including − 7 to -40% rainfall decreases, -24% to -27% number of rainy days decreases and − 2 to -6% lower soil moisture. During a very strong El Niño year, Marathwada experienced a 40% rainfall deficit, 24% reduction in rainy days and a 70% crop yield decline, while Vidarbha had a 7% rainfall deficit, 27% reduction in rainy days and a 57% crop yield reduction. Soil moisture trends indicated declining levels in Vidarbha during critical soybean growth months (June and August), whereas Marathwada showed no significant trend. Rainfall trends revealed an increase in September in Marathwada, affecting crop maturity, while Vidarbha had a beneficial rainfall trend in July, promoting crop growth and soil moisture. Correlations between soil moisture, rainfall, and soybean yield varied, with Marathwada exhibiting correlations of 0.58 for soil moisture, 0.56 for rainfall, and 0.8 for rainy days, and Vidarbha displaying a correlation of 0.29 for soil moisture, 0.53 for rainfall, and 0.66 for rainy days.</p>