The removal of aboveground biomass for biofuel feedstock is potentially detrimental to soil organic matter (SOM) and soil productivity. Our objective was to simulate SOM changes in agricultural soils under various climate, crop rotations, tillage practices, organic amendments, and crop residue managements using the CQESTR model. Long-term experiments (LTE's) at Champaign, IL (1876), Columbia, MO (1888), Pendleton, OR (1931), and Florence, SC (1979) were selected for their documented history of management practice and periodic SOM measurements. Cropping systems were: continuous corn, corn–oat, and corn–oat–clover rotations with grain, straw, stover, and hay removed until 1955 in control (no fertilizer) or manure treatments at Champaign; continuous winter wheat with straw removal before 1950 was selected for crop residue simulation at Columbia; and winter wheat–fallow rotation with either fall burn (no fertilizer) or manure added before plowing in the spring of the fallow year at Pendleton. The first three LTE's were under moldboard plow system. At Florence two residue harvest scenarios were implemented on plots doubled-cropped with maize–winter wheat followed either by cotton or soybeans under two tillage practices, disking (DT) and conservation tillage (CS). CQESTR captured year to year variation in SOM content well for all sites. A decline in SOM content was observed, and simulated by CQESTR, with crop residue removal under all managements at Columbia, Champaign and Pendleton. At Florence, CQESTR predicted 3.2 and 7.7 g SOM/kg losses under DT and CS, respectively, during 23-yr of 66% residue harvest. The relationship between the SOM changes and corresponding estimates of crop residue and manure applied to soils suggests that a minimum of 8 Mg/ha/yr of crop residue and organic amendment is required to maintain SOM level at Champaign. The quantities of crop residue that can be sustainably harvested are directly influenced by initial SOM concentrations.