Tuberous roots of African geranium (Pelargonium sidoides DC.) with modern ethanolic formulation called EPs 7630 (Umckaloabo) have widely used in medicinal industries. The present study was aimed to explore changes in the phytochemical traits (i.e., phenolics, flavonoids, coumarins and hydroxycinnamic acid derivatives), protein content, enzymatic-antioxidants and antimicrobial activities of several high-yielding hairy root lines (HRLs) of P. sidoides harvested at different times. Among all HRLs, antioxidative responses (e.g., phenylalanine ammonia lyase, polyphenol oxidase and catalase contents) were increased in HRL10 exposed to higher interval harvests. Moreover, HRL10 exhibited a promising antimicrobial effect against Escherichia coli, with MIC equal to (2.61 mg/ml). In total 10 phytochemical compounds were identified through chromatographic (HPLC) technique including: umckalin (Um), gallic acid (GA), quercetin (QE), luteolin (LU) and the others. The extraction of HRs had high content of Um at 21 days (0.35 𝜇g/ml). The maximal phenolic yield in particular GA was enhanced to (5194.5 𝜇g/ml), about 10-fold in comparison with non-transformed roots (516 𝜇g/ml) on the 35th day. HRs were able to produce the maximum improvement in flavonoid glycosides (13.96 𝜇g QE/ml and 23.75 𝜇g LU/ml) at the end of culture period. The most profitable transgenic lines offers an interesting option to enhance the productivity. These results support the in vitro cultivation of HRs for supply as a natural product to prevent inflammation and microbial related disorders.