Secondary metabolites were isolated using chromatographic techniques after being extracted sequentially from the roots of Artemisia afra using organic solvents such as ethanol, ethyl acetate, dichloromethane, and n-hexane. The isolated compounds were evaluated for anti-fungal, anti-bacterial, and cytotoxicity activities. Spectroscopic techniques, including Nuclear Magnetic Resonance (NMR), Fourier transform infrared (FTIR), and liquid chromatography–mass spectrometry (LC-MS), were used to elucidate the structures of the isolated compounds. The phytochemical investigation of A. afra led to the isolation of eight (A–H) compounds which were identified as 3β-taraxerol (A), 3β-taraxerol acetate (B), dodecyl-p-coumarate (C), ferulic acid (D), scopoletin (E), sitosterol-3-O-β-D-glucopyranoside (F), 3,5-di-O-feruloylquinic acid (G) and Isofraxidin-7-O-β-D-glucopyranoside (H) based on spectroscopic data. Compounds A, B, C, F, G, and H are known but were isolated for the first time from the roots of A. afra. The isolated compounds and extracts from A. afra exhibited good anti-fungal and anti-bacterial activity with dichloromethane and ethyl acetate crude extracts (0.078 mg/mL) and compound E (62.5 µg/mL) showed good activities against Escherichia coli. Compounds C and F also showed good activity against Enterococcus faecalis with minimum inhibitory concentration (MIC) values of 62.5 and 31.25 µg/mL, respectively. Extracts and compounds (A–H) exhibited anti-fungal and anti-bacterial properties and showed no toxicity when tested on Vero monkey kidney (Vero) cells.