Autumn-planted cover crops are used to improve soil quality and crop productivity, however the assessment of soil quality for cover cropping systems has typically involved the use of destructive methods. This study was conducted to evaluate the effect of cover crop and corn stover residue decomposition on soil quality in a Brookston sandy loam. The field experiment consisted of a split-plot design with cover crops planted in autumn 2007-2010 as main plot factor, and the presence or removal of corn stover in autumn 2011 as split-plot factor. Cover crop treatments included a control with no cover, oat (Avena sativa L.), cereal rye (Secale cereale L.), oilseed radish (Raphanus sativus L. var. oleoferus Metzg. Stokes), and a mixture of oilseed radish and cereal rye  planted at 81, 67, 16, and 9+34 kg ha^-1, respectively. In autumn 2012 after squash production, composite soil samples were extracted (0-15 cm) from subplots and mixed with dried, ground cover crop biomass based on mean above-ground biomass yields (3100 to 3600 kg ha^-1). Mixed soils were weighed (250 g), adjusted to 60% water holding capacity, placed in microcosms, incubated at 22±3˚C for 72 d, and sampled 13 times during the incubation period. Diffuse Reflectance Infrared Fourier Transform (DRIFT) technique was used to assess average spectral peak area for active and inactive soil carbon fractions. A decomposition curve was established for polysaccharide-C (950-1050 cm^-1) spectral region and was compared to C and N mineralization rates from destructive sampling methods (microbial biomass C and soil mineral nitrogen). Preliminary results of spectral datum indicated differences between corn stover treatments (removed vs left) with polysaccharide-C bands peaking at 2 d and plateauing in 15 to 35 d. In this study, DRIFT spectroscopy represented a rapid and accurate non-destructive method to assess cover crop decomposition in a soil matrix.