Thermochemical conversion of agricultural wastes to bioenergy has a potential to play forefront roles within the context of the food, energy, and water nexus. The biochar solid product of pyrolysis is a promising tool to manage food crop production and water resources by means of soil amendment. The goal of this study was to understand the fate of surface functional groups and higher-atomic-mass elements during the pyrolysis of pecan shell, which is known to accumulate calcium oxalate. Pecan shell feedstock and biochars were analyzed ex situ using X-ray computed microtomography and solid-state C-13 cross-polarization and magic-angle-spinning NMR spectroscopy; the pyrolysis kinetics was monitored in situ by thermogravimetric analysis gas chromatography (TGA-GC). The NMR spectra indicated the greatest (i) reduction in O/N alkyl functionality and (ii) increase in the aromatic peak between 300 and 500 degrees C. Primary physical transformation was observed near 400 degrees C in the tomography slice images and corresponding attenuation coefficients. Key changes in physical structure (microtomography) as well as chemical constituents (solid-state NMR) of pecan shell at 300-500 degrees C coincided with the evolution of gaseous products (hydrogen, methane, carbon monoxide, carbon dioxide, ethylene, and ethane, as monitored in situ by TGA-GC) occurring at 200-500 degrees C. These observations followed the reported (0 formation and removal of carboxyl surface functional groups of biochar and (ii) conversion of calcium oxalate to carbonate, both occurring at the key transition temperature near 400 degrees C. Combined with the mass balance (99.7%) obtained for gas-, liquid-, and solid-phase products, these findings will facilitate reactor design to optimize syngas and bio-oil yields and manipulate the surface reactivity of biochar soil amendment.