In this study, the extraction conditions of bioactive aglycones from a celery extract supplemented with germinated soy were optimised by a response surface methodology. For subsequent enzymatic hydrolysis to enhance the apigenin content, increased production of its precursor apigetrin was firstly achieved through acidic extraction at optimal conditions, involving water at pH 1, at 75 °C for 2 h. Subsequently, a central composite design was conducted to analyse the pH (3–11) and temperature (25–35 °C) effects on the aglycone levels (apigenin, daidzein and genistein). The optimal extraction conditions were pH 7.02 and 29.99 °C, which resulted in a 40-fold increase in apigenin. The novel and cost-effective application of germinated soy β-glucosidase for the conversion of aglycones in non-soy foods is demonstrated. The enhanced bioactivities of aglycones may suggest potential applications for similar formulations as functional food ingredients.