An increasing demand for natural flavonoids necessitates the development of new technologies to improve the extraction of phytochemicals whilst retaining their bioactivity. Extracts from rooibos (Aspalathus linearis), well known as an herbal tea and food and beverage supplement, have shown significant potential for the treatment of various lifestyle conditions, but poor extraction of soluble matter limits its potential value and put limited supplies under pressure. This study demonstrates that pre-treatment with food-grade cellulase, ferulic acid esterase and/or pectinase increased the soluble solid yield from green and fermented rooibos when preparing an infusion, whereas ferulic acid esterase and β-glucanase/β-xylanase increased the total polyphenol yield. A combination of β-glucanase/β-xylanase and pectinase increased the yield of soluble solids from fermented rooibos in industrial evaluations by 33%. Although the total polyphenol and antioxidant content was reduced due to the extraction of ‘inactive’ sugar moieties, the extract exceeded industry benchmarks for both quality parameters. Furthermore, a clear extract was produced with no detrimental impact on its sensory attributes. Although the enzyme treatment reduced the aspalathin content of the extract, there was a concomitant increase in its flavone counterpart, isoorientin, which has significant pharmaceutical value for the treatment of both types of diabetes mellitus.