Lignin-first biorefining constitutes a new research field in which the overarching objective is the prevention of lignin recalcitrance while providing high-quality pulps. For this purpose, the solvent extraction of lignin is performed in the presence of a hydrogenation catalyst, employing H2 pressure or an H-donor solvent (e.g., 2-propanol), and thus leading to passivation of reactive lignin fragments via reductive processes. As a result, lignin-first biorefining methods generate high-quality pulps in addition to low-molecular-weight lignin streams with high molecular uniformity. Nonetheless, upon cooking lignocellulose in solvent mixtures containing water, other processes on the lignocellulosic matrix take place, releasing soluble intermediates. In fact, hemicellulose undergoes deacetylation, to a variable extent, releasing acetic acid into the liquor. Moreover, formic acid can also be formed as a degradation product of hemicellulose C6-sugars also released into the liquor. However, despite this general notion, the formation and fate of these carboxylic acids during the cooking of lignocellulosic substrates, and the effects these acids may have on hydrogenation catalyst performance remain poorly understood. In this report, we examine both the formation and subsequent fate of formic acid and acetic acid during lignocellulose deconstruction for both a lignin-first biorefining method (via H-transfer reactions in the presence of Raney Ni catalyst) and its equivalent Organosolv process with no added acid or hydrogenation catalyst. A mechanism for the mitigation of formic acid formation in the presence of Raney Ni catalyst is outlined via the hydrogenation of sugars to sugar alcohols. Furthermore, the effects of the carboxylic acids on Raney Ni performance are assessed, using the transfer-hydrogenation of phenol to cyclohexanol/cyclohexanone as a model reaction, elucidating inhibition rates of the acids. Finally, we conclude with the implications of these results for the design of lignin-first biorefining processes. In a broader context, understanding of the formation and fate of carboxylic acids during CUB is crucial to producing high-quality pulps with high degrees of polymerization and high xylan contents.