We previously demonstrated that a two-stage pretreatment comprising of an alkaline pre-extraction followed by a Cu-catalyzed alkaline–oxidative treatment is effective at pretreating hardwoods under relatively mild reaction conditions. In this work, we focus on characterizing how biomass source and reaction conditions used during the alkaline pre-extraction impact the subsequent processing stages as well as lignin yields and properties. Specifically, three hybrid poplars were subjected to the first stage alkaline pre-extraction under various conditions including differences in time (15–300 min), temperature (95–155 °C), and alkali loadings (50–200 mg NaOH/g biomass), and the impact on total mass solubilization, lignin recovery, and lignin purity was determined. Empirical correlations were developed between reaction conditions and mass solubilization and lignin recovery during the pre-extraction stage. For select conditions, lignin properties were assessed and include β-O-4 content determined by 13C NMR, molecular mass distributions as determined by gel permeation chromatography, and susceptibility to depolymerization to aromatic monomers using thioacidolysis and formic acid catalyzed depolymerization. We found alkaline pre-extraction performed at higher temperatures generated lignins exhibiting lower contamination by polysaccharides, lower aromatic monomer yields from depolymerization, lower molar masses, and lower β-O-4 contents relative to the lower temperature pre-extractions. Finally, the pre-extracted biomass from select conditions was assessed for its response to the subsequent Cu-catalyzed alkaline–oxidative treatment and enzymatic hydrolysis. It was demonstrated that minor differences in delignification during pre-extraction have quantifiable impacts on the subsequent efficacy of the second stage of pretreatment and enzymatic hydrolysis with improved lignin removal during the first pre-extraction stage resulting in improved hydrolysis yields.