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Hydnora johannis is a medicinal plant traditionally used to treat various ailments. Chemical investigation of the dichloromethane (DCM)/methanol (MeOH) (1:1) roots extract of Hydnora johannis afforded three compounds (1–3), reported herein for the first time from the species. The structures of the isolated compounds 1–3 were elucidated using 1D and 2D NMR spectroscopic analysis and comparison with literature data. The highest zone of inhibition value was measured for DCM/MeOH extract (10.75 ± 0.25 mm) against Staphylococcus aureus at concentration of 0.25 mg/mL, promising in comparison to the standard amoxicillin (16.0 ± 0.0 mm, 0.25 mg/mL). At concentration of 0.25 mg/mL, the largest mean inhibition zone of 12.0 ± 0.0 mm was measured for compound 2 against Pseudomonas aeruginosa, comparable to the standard drug amoxicillin (16.0 ± 0.0 mm, 0.25 mg/mL). Compound 2 displayed better binding affinity with minimum binding energy of − 8.7 kcal/mol (PqsA), − 7.6 kcal/mol (DNA gyrase), and − 7.4 kcal/mol ( S aureus PK) than amoxicillin (− 7.3, − 6.1, and − 7.0 kcal/mol, respectively). This suggests that compound 2 may act as potential inhibitor of the tested bacterial proteins. Compound 1 satisfies the Lipinski’s rule of five with zero violations. Compound 2 obey the MW (452.4 g/mol) and iLogP (< 5) rules, and compound 3 obey the NHD (4) and NHA (6) rules. Compounds 2 recorded iLogP value less enough than five (1.55), implying its optimal lipophilicity. Compounds 1 and 3 satisfy the veber’s rule (NRB < 12, and TPSA < 140 unit). Compound 2 and 3 exhibited negligible acute toxicity (LD50 > 5000, Toxicity class > 5. Compound 2 demonstrated maximum scavenging activity (67.87%) with IC50 value of 0.190 µg/mL, compared to ascorbic acid (78.21%) with IC50 value of 0.014 µg/mL at concentration of 12.5 µg/mL. Overall, the in vitro antibacterial activity of the extracts and compounds, molecular docking analysis and radical scavenging activity results of the isolated compounds suggest DCM/MeOH crude extract and compound 2 are promising antibacterial agents whereas compound 2 and 3 are promising antioxidants which corroborates with the traditional uses of the roots of H. johannis.

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