Biomass is an attractive source of renewable carbon-based fuels and chemicals. Multiple research efforts are centered around integrated biorefineries, where all fractions of biomass are converted to fuels or chemical products. These efforts are focused around making biorefineries more economically competitive and sustainable. One of the major drawbacks is the incomplete utilization of biomass, specifically, lignocellulosic biomass, which is the largest terrestrial source of renewable carbon. Given the significant differences in the structure and reactivity of its components, the integrated depolymerization and subsequent upgrading of all the fractions involved has been challenging. The depolymerization of lignocellulosic biomass is controlled by the kinetic competition between depolymerization and degradation reactions. Multiple strategies have relied in the modification of reaction conditions to mitigate this limitation, but are either expensive or have not fully overcome this issue. Here, I present the use of protecting group chemistry to reversibly stabilize biomass-derived carbohydrates during depolymerization by acetal formation with formaldehyde (FA). This stabilization technique, altered the kinetic paradigm by limiting sugar dehydration and further degradation. The depolymerization of beech wood using acid organosolv processes in the presence of FA led to recoveries of over 90% sugars with a final concentration of ~5wt%. The produced acetal-stabilized biomass-derived sugars possess versatile properties compared to unmodified sugars, which motivated me to further investigate their reactivity. I found that diformylxylose (acetal-stabilized xylose, DX) produced an intermediate during its acid hydrolysis deprotection that promoted a 1,2-hydride shift that led to the low temperature production of furfural. Generally, this shift is catalyzed by Lewis acids, but its presence did not affect the rate of reaction when DX was used as a starting material. Based on these findings and Operando NMR studies, a tandem hydrolysis-dehydration of DX to furfural, was pro-posed. The benefits of using acetal-stabilized sugars was studied by performing a preliminary techno-economic analysis for the non-enzymatic production of ethanol and the direct upgrading of DX to xylitol. After taking account the solvent savings and the extra recovery steps of FA, a minimum selling price of $4.05 ($2014) of gasoline gallon equivalent was calculated. In the case of xylitol production, a proposed process was constructed around the volatility and unique reactivity of DX. The key advantages included the purification potential of DX by distillation rather than activated carbon adsorption and ion exchange chromatography, which is used for xylose purification, and a rate limiting step that was independent of hydrogen pressure, which minimized hydrogen requirements. The on stream study of the catalyst demonstrated an evolution of the active sites of Pt that led to an enhanced xylitol yield. This phenomenon is attributed to the formation of Pt(OH)2 (detected by X-ray photoelectron spectroscopy), which accelerates the hydrolysis and hydrogenation reactions due to the proximal acid site to Pt0. In overall, I have demonstrated that acetal functionalization of carbohydrates can, not only increase yields by reducing sugar degradation but also reveal new reactivity that can be exploited to create novel catalytic upgrading pathways for the production of bio-based chemicals.