The in vitro cultures of the following three species of the genus Ruta were investigated: R. chalepensis, R. corsica, and R. graveolens. The dynamics of biomass growth and accumulation of secondary metabolites in the 3-, 4-, 5-, 6-, and 7-week growth cycle were analysed. The antioxidant capacity of the methanol extracts obtained from the biomass of the in vitro cultures was also assessed by different in vitro assays: 1,1-diphenyl-2-picrylhydrazil (DPPH), reducing power, and Fe²⁺ chelating activity assays. Moreover, a preliminary screening of the antimicrobial potential of the extracts was performed. The extracts were phytochemically characterized by high-performance liquid chromatography (HPLC), which highlighted the presence of linear furanocoumarins (bergapten, isoimperatorin, isopimpinellin, psoralen, and xanthotoxin) and furoquinoline alkaloids (γ-fagarine, 7-isopentenyloxy-γ-fagarine, and skimmianine). The dominant group of compounds in all the cultures was coumarins (maximum content 1031.5 mg/100 g DW (dry weight), R. chalepensis, 5-week growth cycle). The results of the antioxidant tests showed that the extracts of the three species had varied antioxidant capacity: in particular, the R. chalepensis extract exhibited the best radical scavenging activity (IC₅₀ = 1.665 ± 0.009 mg/mL), while the R. graveolens extract displayed the highest chelating property (IC₅₀ = 0.671 ± 0.013 mg/mL). Finally, all the extracts showed good activity against Staphylococcus aureus with MIC values of 250 μg/mL for the R. corsica extract and 500 μg/mL for both R. graveolens and R. chalepensis extracts.