Indian agriculture has long depended on chemical fertilizers to sustain food production; however, their continuous, indiscriminate and imbalanced use has caused nutrient depletion, organic carbon loss, and decline in soil microbial activity, jeopardizing long-term productivity. To counter these challenges, integrated nutrient management approaches that combine inorganic fertilizers with organic and biological inputs are gaining importance. Microbial-enriched manures and nano-emulsion biofertilizers, in particular, are promising options for enhancing nutrient availability, stimulating crop growth, and restoring soil health while reducing dependence on synthetic fertilizers. A field study was conducted during the winter (Rabi) season of 2023–24 at Coimbatore, Tamil Nadu, India, to evaluate the effects of microbial-enriched organic manures and nano-emulsion biofertilizers on soil fertility, microbial dynamics, and chickpea (Cicer arietinum L.) productivity under irrigated conditions. The experiment, laid out in a randomized block design with twelve treatments, combined varying levels of recommended fertilizer dose (RDF) with farmyard manure, vermicompost, microbial-enriched amendments, and nano-emulsion formulations. Results revealed that application of 100% RDF + microbial-enriched vermicompost (6 t ha⁻¹) significantly improved plant growth, dry matter accumulation, physiological indices, nutrient uptake, and microbial activity, producing a higher grain (1276 kg ha⁻¹) and stover yield (2569 kg ha⁻¹). Soil analysis confirmed improvements in organic carbon, available nutrients, microbial biomass, and enzymatic activities under this treatment. Economic evaluation showed that, while this combination achieved maximum gross returns (INR 95,700 ha⁻¹), the treatment with 75% RDF + nano-emulsion biofertilizer delivered superior net returns (INR 56,785 ha⁻¹) and benefit–cost ratio (2.72). The integration of microbial-enriched vermicompost with recommended dose of fertilizers (RDF) significantly improves chickpea yield and soil health, while partial replacement of RDF with nano-emulsion biofertilizers presents a viable, economical, and eco-friendly alternative.