Allochrusa gypsophiloides is a rare Central Asian species, a super-producer of triterpene saponins with pharmacological and technical value. In this work, a comparative evaluation of the in vitro culture of adventitious roots (ARs), in vitro adventitious microshoots (ASs), natural roots and aboveground parts of wild plants from Kazakhstan to define the total saponin (TS), phenol (TP) and flavonoid (TF) content, as well as antioxidant (AOA) and antimicrobial activity, is presented for the first time. In the AR culture, growth index (GI), TS, TP and TF were evaluated on days 25, 45 and 60 of cultivation on ½ MS medium without (control) and with auxin application. It was found out that TS and TF were higher in the in vitro AR culture. The amount of TP and TF are higher in the aerial part of vegetative plants with maximum AOA. The concentration of the extract required to inhibit 50% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical formation (ICO50) in extracts from natural material negatively correlated with TS, TP, TF and in the in vitro AR culture with TF. Control extracts from the in vitro AR culture with high TS levels showed growth-inhibitory activity against S. thermophillus, S. cerevisiae and C. albicans. The influence shares of medium composition factor, cultivation duration factor and their interaction with GI, TS, TP and TF were determined. The in vitro AR culture is promising for obtaining triterpene saponins TSR with high antibacterial and antifungal activity, and the in vitro ASs culture—for shoot multiplication with antioxidant properties.