The present study evaluates the synergistic application of an anaerobic digestate for enhanced rice yield. The study utilised the digestate as a fertiliser with various inoculum-to-substrate (IS) ratios of anaerobic digestion from cow dung and water hyacinth (CW–BF) with combinations of NPK (16-22-22) fertiliser for rice yield optimisation. The outcome of the combined digestate and fertiliser application on rice cultivation was observed in terms of parameters such as the number of tillers, panicle number, panicle length, fertile panicles, and 1000-grain weight. The digestate combination of CW–BF:NPK (3:1:1) resulted in the highest grain yield (7521 kg/hectare) with increased panicle length, test weight, and more filled grains than the other combinations. Moreover, various machine-learning approaches were used to study the efficacy of the different combinations of applied fertiliser (cow dung, water hyacinth, and NPK). The gradient-boosting machine-learning model was appropriate for predicting the modelling based on the measured data. Principal component analysis revealed NPK as the first principal component with high loading values and the digestate as the second principal component, which indicates its crucial role in fertiliser preparation. Therefore, deploying such hybridised fertilisers using the proper statistical analysis and machine-learning approaches can improve rice yield, which would be essential for the socio-economic uplifting of marginal rice farmers.