Biochar research is still in its infancy and fundamental questions such as how and why biochar amendments might confer their proposed beneficial properties to soils remaining unanswered. Most studies have been limited to discussions of changes in the bulk characteristics of biochar and soil after incubation however investigations at the nano- and micro-scale levels are critical to elucidating processes responsible for long term stabilization of biochar in soils and subsequent role in climate change mitigation through N cycling and C sequestration. Synchrotron based infrared and X-ray techniques offer the needed combination of time and spatial resolution required to investigate molecular- and atomic-scale variations of C forms at the soil/biochar interface to reveal specific mechanisms of binding. The overall objective of our research is to elucidate molecular-level interactions involved in the stabilization of biochar, originating from various organic residues, with time. Laboratory incubations (30, 60, 180 and 365d) of three biochars [walnut shell (900° C), wood feedstock (700 and 900° C)],  both alone and in Yolo silt loam were conducted in the dark at 25° C with water content maintained at 55-60% of water filled pore space. Molecular-level interactions involved in the stabilization of biochar were investigated using Scanning Transmission X-ray Microscopy (STXM) and Synchrotron Fourier Transform Infra-red Spectroscopy (SR-FTIR). The STXM data show an increase in prominence of C=C unsaturated/ aromatic carbon (287.3 eV) with respect to aliphatic carbon (285.3 eV), an increase in surface carbon functionality and an increase in oxygen substituted carbon (C-OH, C-OR and C-O-C) as a function of time.  The importance of these groups was also evident in the corresponding SR-FTIR data (peaks at 1730 and 1160 cm^-1); suggesting bonding via these functional groups may be responsible for biochar stabilization in soil.