Soil organic matter (SOM) is important to cropping system sustainability because it stores nutrients and improves soil structure. Alternative cropping systems have been designed to accumulate SOM. The challenge in determining nutrient availability in these systems lies in (1) assessing the temporal availability of nutrients; (2) determining the interaction of fertilizer N with organic N pools; and (3) determining the relationship of SOM turnover dynamics to nutrient availability. We have shown previously that conventional fertilizer N is more available than cover crop N for initial crop uptake. In contrast, the cover crop N displays a more sustained release over the growing season. Besides showing distinct temporal patterns of N availability from these different sources of N, when added together the fertilizer sources show a strong interaction changing their availability. Under the conditions of this study, 2 crop inputs (mineral fertilizer or aged manure) complementary to a vetch cover crop were found to increase net recovery of vetch-derived N in a corn crop. The effect of vetch on the corn crop uptake of fertilizer-N, however, was negligible. Though both observations help describe a unique scenario of microbial dynamics, these observations are net results, and the exact progress of microbial dynamics in each system is not certain. The most profound changes in SOM occurring during this study were observable by simple analysis of the whole soil (the sum of all pools). Other effects were identified only upon fractionation (chemical fractionation, in this case). Our results suggest that SOM and its fractions may respond more dynamically than commonly thought to changes in external inputs and conditions. However, it remains a challenge to predict nutrient availability from distinct SOM fractions. An increased understanding of fertilizer interactions and SOM maintenance is required in order to develop optimum agricultural practices to sustain alternative cropping systems.