A field experiment was started in 2008 under All India Co-ordinated Research Project- Soil Test Crop Response in western Rajasthan to study the long-term effects of nutrient management strategy using Soil Test Crop Response (STCR) approach on cluster bean– wheat cropping system. The present investigation indicated effects of organic compost and inorganic fertilizer as per soil test crop response approach basis on soil carbon dynamics. The treatments consisted of general recommended dose, target yield 15 q ha-1, target yield 15 q ha-1 with Integrated Plant Nutrient System (IPNS), target yield 20 q ha-1 and target yield 20 q ha-1 without Integrated Plant Nutrient System. The soil organic pools were studied after 9 years and it was found that the total C and its different pools of soil increased significantly under target yield 20 q ha-1 with IPNS. Active and passive pools (AP and PP) of carbon of soil increased significantly under target yield 20 q ha-1 with IPNS as compared to the target yield 15 and 20 q ha-1 treatments without IPNS and at par with target yield 15 q ha-1 with IPNS. Carbon management index (CMI) and carbon stock (CS) increased significantly under target yield 20 q ha-1 with IPNS. It can be concluded that combined application of organic and inorganic nutrient in long term basis significantly enhance carbon sequestration rate, consequently soil quality.