The effects of UV-C irradiation (at doses of 8.16, 10.93, 16.17, and 33.29 mJ/cm2) on the physicochemical and microbiological properties of Agave tequilana Weber extracts at various pH values (4.5, 5.5, and 6.5) were evaluated. Thermal treatment (TT) was used as a control (85 °C for 30 s). Both processed (UV-C or TT) and unprocessed (UP) extracts were investigated. The UV-C dose and the pH significantly (p < 0.05) affected the inactivation of total coliforms (TC), total aerobic mesophiles (TAM), and yeasts and molds (YM). UV-C doses of 10.93 mJ/cm2 at pH 4.5 and 33.29 mJ/cm2 at any agave extract pH completely inactivated the native microbial load compared to TT. The total polyphenols (TP), antioxidant activity (AA), and sugar content did not change in the agave extracts at any dose, but the total flavonoid (TF) content decreased at doses > 16.17 mJ/cm2 at the evaluated pH values. Although the color of the agave extracts (L*, a*, and b*) was significantly affected, the total color difference (∆E) did not change after processing compared to the ∆E in the UP extracts. TT further reduced all the physicochemical properties of the agave extracts compared to UV-C processing. The results suggest that UV-C continuous flow technology can be used to stabilize agave extracts at doses of 10.93 mJ/cm2 and pH 4.5, while preserving their functional properties.