To intensify rainfed dryland agriculture sustainably, nutrient management practices that improve soil health without compromising productivity are needed. This study evaluated the long-term effects of fertiliser application in conjunction with the short-term application of nutrient-enriched nanoclay biopolymer composites (NCPCs) on soil properties, nutrient dynamics and crop productivity in a rainfed rice-lentil system. The experiment was conducted in a 38-year-old long-term fertiliser trial with the following treatments: control (no applied nutrients), 100 % recommended dose of fertiliser (RDF) (80:40:30 kg N:P2O5:K2O ha-1), 50 % RDF, 50 % RDF+ 50 % nitrogen (N) (foliar spray), 50 % farmyard manure (FYM), 100 % FYM at 5 t ha-1, 50 % RDF + 50 % FYM and farmer practices as a main plot treatments, along with different NCPC treatments as subplot treatments under split plot design during 2023 and 2024. The integrated application of 50 % RDF and 50 % FYM improved soil physicochemical and biological properties and increased the active carbon pool (30 % of the total organic carbon) and the lability index (0.97) compared to the control. The conjunctive use of 50 % RDF and 50 % FYM produced the highest rice yield (2246 kg ha-1), lentil yield (952 kg ha-1) and system equivalent rice yield (5019 kg ha-1). The application of NCPC resulted additive effects, such as molybdenum/Arthrobotrys oligospora-loaded composites enhanced lentil productivity, whereas potassium- and zinc-loaded composites improved nutrient uptake. The integration of long-term organic-inorganic fertilisation with nano-enabled nutrient and microbial delivery system improved biological functioning and system productivity of rice under rainfed conditions of the Indo-Gangetic plains.