Chemical investigation of the fruit peel of dietary plant Citrus hystrix offered two new flavones 5,6,4′-trihydroxypyranoflavone I and 5,4′-dimethyl-6-prenylpyranoflavone XIII besides 11 known compounds. The structures of all compounds were elucidated with the aid of suitable analytical methods like 1D, 2D-NMR, mass and single crystal X-ray analysis. An X-ray crystal study of compound II was done for the first time and the compounds I–VI, XI and XII are hitherto not reported from this plant. Biological studies revealed that compound I found to have a good antidiabetic and antiacetylcholinesterase activities meanwhile compounds II, III and V showed a significant free radical scavenging ability as well as antioxidant capacity. In addition, compounds I, IV, V and VI showed cytotoxicity against U87, A549 and MCF-7 cells. Overall, the new compound I showed valuable bioactive properties. Due to insufficient quantity of compound XIII, biological studies were not done.