The intercropping cultivation system on rainfed land during the dry season often faces water availability constraints and declining soil fertility, which negatively affect crop productivity. The use of manure and liquid bio-fertilisers is one approach to increase the soil’s organic matter content and microbiological activity, thereby improving nutrient availability for plants. This study aimed to analyse the effects of manure and liquid bio-fertiliser dosages, determine the optimum doses of these two inputs, and evaluate their interaction on the yield of five crop commodities in an intercropping system on rainfed land during the dry season. The results showed that crop response to the treatments was commodity-specific. The highest Cucumis sativus L. yield (23.1 t ha⁻¹) was obtained with a combination of 25 t ha⁻¹ manure and 3 L ha⁻¹ liquid bio-fertiliser. In comparison, butternut squash achieved a maximum yield of 15.0 t ha⁻¹ with a combination of 15 t ha⁻¹ manure and 3 L ha⁻¹ liquid bio-fertiliser. For Capsicum frutescens L., the highest yield (0.146 t ha⁻¹) was achieved with a combination of 25 t ha⁻¹ manure and 6 L ha⁻¹ liquid bio-fertiliser. In comparison, Vigna unguiculata L. produced its highest yield (0.70 t ha⁻¹) with the same combination. For Ipomoea aquatica F., the highest biomass yield (6.3 t ha⁻¹) was obtained with a combination of 25 t ha⁻¹ manure and 3 L ha⁻¹ liquid bio-fertiliser. Optimisation analysis indicated that Cucumis sativus L. and butternut squash yields followed a quadratic pattern, with optimum liquid bio-fertiliser dosages of approximately 2.88 L ha⁻¹ and 3.14 L ha⁻¹, respectively. In comparison, the optimum manure dosage for butternut squash was estimated to be approximately 15.19 t ha⁻¹. At the system scale, the intercrop was advantageous under every treatment (LER 1.75–2.95, mean 2.07; ATER 1.30–2.20), with cucumber acting as the dominant component. These results indicate that integrating manure and liquid bio-fertilizers increases the productivity of intercropping systems by improving soil organic matter content and microbial activity under rainfed conditions during the dry season.