Agave lechuguilla agro-waste is a promising renewable material for biorefining purposes. The procurement of added-value co-products, such as bioactive phytochemicals, is required to improve bioprocesses and promote the bio-based economy of the productive areas of Mexico. In this study, we aimed to evaluate the effect of post-harvest management and enzymatic pretreatment as the first stages of the A. lechuguilla valorization process. Four drying methods were compared, and enzymatic hydrolysis was optimized to obtain a flavonoid-enriched extract applying ultrasound-assisted extraction. In both experiments, the total phenolic (TPC) and flavonoid (TFC) contents, HPLC-UV flavonoid profiles, and radical scavenging capacity (DPPH) were considered as response variables. The results demonstrated that light exposure during the drying process particularly affected the flavonoid content, whereas oven-dehydration at 40 °C in the dark preserved the flavonoid diversity and antioxidant functionality of the extracts. Flavonoid glycoside recovery, particularly anthocyanidins, was 1.5–1.4-fold enhanced by enzymatic hydrolysis using the commercial mix Ultraflo© under optimized conditions (pH 4, 40 °C, 180 rpm, and 2.5 h) compared to the unpretreated biomass. The extraction of flavonoids from A. lechuguilla bagasse can be carried out using a scalable drying method and enzymatic pretreatment. This study confirmed the potential of this agro-waste as a source of marketable natural products.