Management of soil organic matter (SOM) is important for soil productivity and responsible utilization of crop residues. Carbon (C) models are needed to predict long-term effects of management practices on C storage in soils and to estimate the benefits when considering alternative management practices. CQESTR, is a C balance model that relates organic residue additions, crop management and soil tillage to SOM accretion or loss. The model works on daily time-steps and can perform long-term 100-year simulations. Soil organic matter change is computed by maintaining a soil C budget for additions such as crop residue or added amendments like manure, and organic C losses through microbial decomposition. Our objective was to simulate SOM changes in agricultural soils under a range of climate and management systems using CQESTR.  Long-term experiments (e.g. Champaign, IL, >100 yrs; Columbia, MO, >100 yrs; Lincoln, NE, 20 yrs) under various crop rotations, tillage practices, organic amendments, and crop residue removal treatments were selected for their documented history of the long-term effects of management practice on SOM dynamics.  Predicted and observed values from the sites were significantly related (r² = 94%, n = 113, P < 0.001) with slope not significantly different from 1. CQESTR successfully simulated a substantial decline in SOM with 50 years of crop residue removal under various rotations at Columbia and Champaign.  The increase in SOM following addition of manure was simulated well. However, the model underestimated SOM for a fertilized treatment at Columbia. Given the high correlation of simulated and observed SOM changes, CQESTR can be used as a tool to predict SOM changes from management practices and offers the potential for estimating soil C storage required for C credits or to estimate impacts of crop residue removal for feedstock for bioenergy production on SOM level and soil production capacity.