The phytochemical investigation of an ethanol extract of Artemisia afra led to the isolation of six known compounds, acacetin (1), 12α,4α-dihydroxybishopsolicepolide (2), scopoletin (3), α-amyrin (4), phytol (5), and a pentacyclic triterpenoid betulinic acid (6). The compounds were evaluated for antimicrobial activity against Gram positive (Actinomyces naeslundii, Actinomyces israelii, and Streptococcus mutans), Gram negative bacteria (Prevotella intermedia, Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans previously known as Actinobacillus actinomycetemcomitans), and Candida albicans. The crude extract of A. afra inhibited the growth of all tested microbial species at concentration range of 1.6 mg/mL to 25 mg/mL. The compounds 1–6 also showed activity range at 1.0 mg/mL to 0.25 mg/mL. Three best compounds (scopoletin, betulinic acid, and acacetin) which showed good antimicrobial activity were selected for further studies. Cytotoxicity of extract and compounds was determined using the XTT cell proliferation kit. The antioxidant activity of the extract and compounds was done using the DPPH scavenging method. The extract showed good antioxidant activity with an IC50 value of 22.2 μg/mL. Scopoletin had a strong transformation of the DPPH radical into its reduced form, with an IC50 value of 1.24 μg/mL which was significant to that of vitamin C (1.22 μg/mL). Acacetin and betulinic acid exhibited a decreased scavenging activity with the IC50 of 2.39 and 2.42 μg/mL, respectively. The extract and compounds showed moderate toxicity on McCoy fibroblast cell line and scopoletin was relatively nontoxic with an IC50 value of 132.5 μg/mL. Acacetin and betulinic acid also showed a smooth trend of non-toxic effects with IC50 values of 35.44 and 30.96 μg/mL. The obtained results in this study confirm the use of A. afra in the treatment of microbial infections.