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Reliable estimation of crop yield is vital for refining farming operations and guaranteeing food supply. This investigation tested the capacity of machine learning techniques to estimate tomato yield using meteorological measurements, spectral reflectance bands, and vegetation indices subjected to different nitrogen levels and bio-stimulant applications to generate variation in crop development. UAV-mounted sensors captured spectral information across seven acquisition dates spanning October 27 to December 15, 2023, matching critical developmental windows: vegetative establishment (acquisition 1), anthesis (acquisitions 2 and 3), fruit set and enlargement (acquisitions 4, 5, and 6), and initial maturation (acquisition 7). Discriminating explanatory variables were selected via the Pearson correlation metric (r > 0.65, P < 0.05), incorporating Near Infrared (NIR), Red Edge, and Red wavebands, together with vegetation indices comprising NDVI, GNDVI, NDRE, and SAVI. Remotely sensed canopy signatures gathered throughout the fruit set and enlargement window (acquisitions 5 and 6) displayed the tightest association with harvested yield (r = 0.66–0.74), reinforcing the necessity of spectral intelligence from the middle to latter parts of the cycle. When comparing predictive algorithms, both linear regression (LR) and XGBoost yielded the strongest predictive skill, producing root mean squared error (RMSE) figures of 16.13 kg and 16.15 kg, respectively, matched with R² values reaching 0.63. Support vector machine (SVM) and decision tree (DT) implementations also delivered competent outcomes, achieving RMSE scores of 17.15 kg and 17.18 kg, respectively. By comparison, the deep learning architecture lagged notably (RMSE = 23.49 kg, R² = 0.23), plausibly attributable to data scarcity. This research spotlights the prognostic capability inherent in spectral wavebands and underscores the centrality of growth-stage-aligned spectral acquisition for yield forecasting.