Raw, mixed and composted organic materials (OM) from agricultural and urban wastes were subjected to biochemical analyses, near infrared (NIR) reflectance spectroscopy and laboratory incubations. Respiration during incubations was accurately predicted using a decomposition model [transformation of added organic materials, (TAO)] of very labile, intermediary resistant, and stable OM fractions. Calibrations using NIR spectra were developed to determine the very labile and stable fractions of OM used to predict three-month OM mineralisation in soil. This study has confirmed that OM decomposition is mainly driven by OM quality on a short-term basis. The wavelengths contributing heavily to the prediction of very labile and stable OM components and molecular functions of these fractions were identified. The resulting TAO–NIR spectroscopy model is an efficient tool to study the degradation of natural molecules and its management for plant growth and sustainability of ecosystems. As a sub-model of a more complex C cycle model, it can instantaneously simulate labile and stable fractions of various organic inputs in soil and, as a non-destructive and easily portable spectroscopic method, could be used to assess C dynamics on a regional scale.