Seven new naphthoquinone diglycosides (<b>1</b>-<b>7</b>), three new anthraquinones (<b>8</b>-<b>10</b>), and eight known analogues were obtained from the aerial parts of <i>Mitracarpus hirtus</i> collected from West Africa in a bioassay-guided phytochemical investigation. All isolated compounds were elucidated by comparison with the literature and interpretation of spectroscopic data, and the absolute configurations of the new naphthoquinone diglycosides (<b>1</b>-<b>10</b>) were confirmed by chemical methods and ECD calculations. Notably, compound <b>1</b> was found to be the first naphthoquinone diglycoside containing carboxylic acid and isopentenyl side chains isolated from a species in the genus <i>Mitracarpus</i>. Compounds <b>6</b>-<b>18</b> showed antibacterial activity against multiple <i>Helicobacter pylori</i> strains with MIC values ranging from 0.0625 to 64 μg/mL. Particularly, 1-hydroxybenzoisochromanquinone (<b>17</b>) and benzo[<i>g</i>]isoquinoline-5,10-dione (<b>18</b>), with MIC values of 0.0625 and 0.125 μg/mL, displayed 32-512-fold higher potencies than a positive control, metronidazole. Compound <b>18</b> also demonstrated high antibiofilm activity and killed biofilm-encased <i>Helicobacter pylori</i> cells more effectively than metronidazole.