Achieving sustainable crop productivity and maintenance of concurrent soil organic carbon (SOC) at desired levels in cereal-based cropping systems in relatively, poorly fertile Vertisols in semi-arid rainfed ecosystem is challenging task for dryland researchers. Different soil fertilization practices can contribute to carbon (C) sequestration, which requires a detailed knowledge of SOC dynamics in soil profile (0–1.0 m). We conducted a field experiment for 6 years to study the effect of applying mineral fertilizers and organic amendments (FYM, compost, green leaf and crop residue) on profile SOC stocks, C sequestration, SOC sequestration rate, C buildup rate and sustainable yield index (SYI) of maize and blackgram crops in dry semi-arid Vertisols of western India. The study encompasses different nutrient management viz., 100% recommended dose of fertilizer (RDF) of NP, 25 kg ha−1 N (FYM) + 25 kg N (Urea) + 30 kg P ha−1, 25 kg ha−1 N (Compost) + 25 kg N (Urea) + 30 kg P ha−1, 25 kg ha−1 N (Crop residue) + 25 kg N (Urea) + 30 kg P ha−1, 15 kg ha−1 N (FYM) + 10 kg N (Crop Residue) + 25 kg N (Urea) + 30 kg P ha−1, 15 kg ha−1 N (FYM) + 10 kg N (Compost) + 25 kg N (Urea) + 30 kg P ha−1, 15 kg ha−1 N (FYM) + 10 kg N (Green Leaf) + 25 kg N (Urea) + 30 kg P ha−1, 100% recommended N (urea) without P and unfertilized control. Randomized Complete Block design was used wherein all the treatments were replicated thrice. Application of 15 kg ha−1 N (FYM) + 10 kg N (Crop Residue) + 25 kg N (Urea) + 30 kg P ha−1 significantly improved the SOC concentration of the soil profile (0–1.0 m) than unfertilized control and treatments receiving solely mineral fertilizers. Highest SOC profile stock, C sequestration with concomitant C buildup was obtained with 15 kg ha−1 N (FYM) + 10 kg N (Crop Residue) + 25 kg N (Urea) + 30 kg P ha−1. A positive correlation is observed between total C input and profile mean SOC content (R2 = 0.74), profile C stock (R2 = 0.76), C sequestration (R2 = 0.76), C sequestration rate (R2 = 0.76) at P values < 0.01. The conjunctive use of 15 kg ha−1 N (FYM) + 10 kg N (Green Leaf) + 25 kg N (Urea) + 30 kg P ha−1 and 25 kg ha−1 N (FYM) + 25 kg N (Urea) + 30 kg P ha−1 resulted in highest mean grain yield of maize and blackgram, respectively, which were significantly superior to treatments receiving mineral fertilization alone. Application of organic amendments in combination with mineral fertilizers was found superior in improving the SYI. Critical C input of 1.14 Mg C ha−1 year−1 is suggested to be added in the soils externally to offset depletion of C and maintaining SOC at equilibrium in the semi-arid Vertisols of western India.