Baby’s breath (Gypsophila paniculata L.) roots are valuable as pharmaceuticals due to the content of triterpenoid saponins and other bioactive phytochemicals. However, the long root harvest period and fluctuation of these constituent’s content are among the constraints to traditional agricultural production. The present study shows an efficient and reliable liquid root culture of G. paniculata cv. ‘Perfecta’ established in a shake flask system using different auxins, media, and sugars. Hairy root (HR) induction in G. paniculata through Rhizobium rhizogenes-mediated transformation was also investigated. α-Naphthaleneacetic acid (NAA) was optimized for adventitious roots (AR) biomass, saponin, and flavonoid production at 1 or 2 mg/L compared to IBA. Full strength Gamborg’s medium (B5) recorded higher saponin content; however, the highest yield of total saponin and total flavonoids was achieved by full strength Murashige and Skoog's (MS) medium. Sucrose was more essential for root growth and accumulated total saponins and flavonoids rather than fructose and glucose. Polymerase chain reaction (PCR) analysis showed that G. paniculata HR carried rolC gene of R. rhizogenes A4 strain in its genome but not virD2 gene. Compared to non-transformed root, saponin content of leaf and stem-derived HR was 2.7 and 2.3-fold, while total flavonoid content was 2.1 and 2.0-fold, respectively. The DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity was also higher in HR extracts than in non-transgenic roots. This study established an efficient protocol for G. paniculata root cultures for sustainable production of important natural saponins and flavonoids.