Ziziphora species (Lamiaceae) have been used in traditional medicine as sedatives, antiseptics, carminatives, or expectorants. Despite their common applications in phytotherapy, there is still lack of evidence about the composition of their extracts and its impact on biological properties of the plants. The aim of this study was to evaluate the content of Ziziphora bungeana, a less studied species growing in Kazakhstan, using HPLC-ESI-QTOF-MS/MS instrumentation and to determine its antimicrobial, antioxidant, and cytotoxic activity together with inhibitory properties against tyrosinase and toxicity in erythrocyte lysis assay. Extracts from Z. bungeana were found to be sources of flavonoids, phenolic acids, organic acids, and terpenes that determined their antiradical activity. The minimum inhibitory concentrations of extracts were lower for Gram-positive bacteria (1.25–10 mg/mL) than for Gram-negative bacteria and fungi (5–20 mg/mL). The EC50 value calculated for antiradical activity ranged between 15.00 ± 1.06 µg/mL and 13.21 ± 3.24 µg/mL for ABTS and DPPH assays, respectively. Z. bungeana extracts were found to decrease the activity of tyrosinase by 50% (at 200 µg/mL) similarly to kojic acid and were slightly cytotoxic for human melanoma A375 cell line (at 200 µg/mL) with no effect on HaCaT keratinocytes. In the end, Z. bungeana did not reveal toxic effects in hemolytic assay as compared to the positive control Triton X-100. The performed tests show potential application of the plant in the treatment of infectious diseases, disorders caused by free radicals, and skin problems.