Growing interest in biomass for bioenergy production has prompted the need for studies that evaluate the effect of above-ground biomass removal on soil quality, especially Soil Organic Matter (SOM), in agricultural systems. The objective of this study is to identify management practice effects on SOM with and without above-ground biomass removal. A multifactor 40-year field experiment conducted in Kompolt, Hungary on a carbonate-free, slightly acidic chernozem brown forest soil was used to address this objective. Samples were taken in four sampling years. Combinations of the following management factors resulted in 54 different treatments with four replications. Those factors included: three crop rotations; manure application (34.5 Mg ha^-1 farmyard beef manure); mineral fertilizer application (236 kg ha^-1 NPK mix that contained 88 kg N ha^-1, 44 kg P2O5 ha^-1, and 104 kg K2O ha^-1); fertilizer application timing; and above-ground biomass management [removal (BR) vs. incorporation (BI)]. Interactions involving manure and mineral fertilizer application, fertilizer application timing, biomass management, and sampling year were significant. Of six management combinations that included a 4-year alfalfa (Medicago sativa L.) stand, five resulted in significantly higher SOM than the comparable management without alfalfa. Timing of manure and manure+NPK significantly affected SOM levels. Mean SOM levels, as affected by management combinations, had the following sequence: NPK+BR<BI<NPK+BI<manure+BR<NPK+manure+BR. SOM (%) for these treatments were 2.82<2.87<2.88<2.91<2.92 respectively. Manure had the most profound effect because its significance was most consistent across a range of management combinations and years. The greatest increase in SOM levels resulted from manure+NPK+BR, however, this combination was not significantly different from manure+BR. These results suggest that agricultural management systems that include alfalfa and manure application have the potential to sustain SOM levels with concurrent above ground biomass removal in continental climates on chernozem brown forest soils with near level topography.