In an attempt to support the push for second generation biofuels in the United States, this research investigates the role that soil organic matter plays in explaining changes in technical efficiency and agricultural productivity across counties in Nebraska. We estimate optimum biomass harvest potentials for forty seven counties in Nebraska. These estimates reveal the percentage of biomass that can be harvested that would not negatively affect current levels of agricultural production. We also give an account of the status of inter-county changes in agricultural productivity in Nebraska. We use an output measure of technical efficiency from non-parametric data envelopment analysis to estimate technical efficiency measures. Total factor productivity change was estimated using an output-based Malmquist index approach. Biomass harvest potentials were obtained by shrinking/contracting only soil organic matter in our linear programming constraints. Results show that SOM does contribute to explaining changes in technical efficiency and total factor productivity across counties in Nebraska. Also, an average measure of TFP growth of 3.7% was obtained for the 41 years period, 99% of which was accounted for by technological change while the contribution of efficiency change was very minimal. 55% of counties in Nebraska have zero harvest potentials while only 45% of counties have excess biomass potentials for harvest. The highest average potential of 35% was reported for Lincoln, Cass, Gosper and Colfax counties.