Structurally unique isopentenyl flavonoids are extremely low in natural plant species, and their cumbersome chemical pathways, scarcity of donors, and poor stability have severely hindered their application scenarios. Xanthohumol (XN), an isopentenyl chalcone, is a unique and abundant herbal efficacy substance in hops (Humulus upulus L.), which is an herb with a variety of clinical benefits. However, 90% of XN is left behind in the production of hop residue, resulting in a waste of natural resources. The poor water solubility and low bioavailability of XN also limit its wide application. Combined biotransformation strategies can greatly enhance the added value of resource materials and become one of the important means for the sustainable utilization of traditional Chinese medicine resources. In this study, an extreme microbial screening strategy for efficient bioconversion of phrenylflavonids is established to achieve Bacillus zanthoxyli GQ8 obtained from brewer's dregs and a non-aqueous biosynthesis system of xanthohumol glycosides (XNG, substrate concentration of 0.5 g/L, conversion rate of 73.2%) is constructed by GQ8. With HT22 cell model of H2O2-induced oxidative damage and BV2 cell model of LPS-induced neuroinflammation, XNG showed little cytotoxicity and exhibited better anti-inflammatory and antioxidant effects compared with the original compound. Our experimental results firstly provide a high-efficiency biotransformation strategy for glycosylation of XN with bacteria and provide a support that prenylflavonoid glycoside derivatives have remarkable biological activity and show better development potential. Display omitted •An extreme microbial screening strategy for efficient bioconversion of xanthohumol is established.•Xanthohumol is converted to xanthohumol glycoside by bacterial for the first time.•The product of Xanthohumol shows significant neuroprotective potential.•Bacillus zanthoxyli GQ8 has substrate hybridity so that realizes the transformation of various flavonoids.