Hypericum perforatum L. hairy root clones cultured under dark (HR1) and photoperiod (HR2) conditions were comparatively assessed for the contents of phenolic compounds and their inhibitory potential against enzymes related to depression, neurodegeneration, diabetes and hyperlipidemia. In silico docking methods were performed to examine the molecular interactions between the preeminent phenolics in HR samples and target enzymes (monoamine oxidase-A, acetylcholinesterase, butyrylcholinesterase, tyrosinase, alpha-amylase, alpha-glucosidase, lipase and cholesterol esterase). Phytochemical analyses showed that HR1 exhibited a better ability for producing vanillic acid, syringic acid, flavan-3-ol derivatives and flavonol glucosides, whereas HR2 were distinguished by their elevated biosynthesis of naphthodianthrones (pseudohypericin and protopseudohypericin) and xanthones. Importantly, photoperiod exposure significantly increased the accumulation of compounds with acetylcholinesterase, alpha-glucosidase, lipase, and cholesterol esterase inhibitory activity. In contrast, HR1 cultures had comparable or even higher monoamine oxidase-A, butyrylcholinesterase, tyrosinase, and alpha-amylase inhibition in comparison to HR2 cultures. When docking data were analysed, procyanidin B2, paxanthone, and garcinone B demonstrated the lowest binding energies towards tested enzymes denoting their contribution to the bioactivities of HR cultures. Outgoing data pointed out that H. perforatum HR cultured under darkness and photoperiod could be considered as a rich source of phenolics with a wide array of biological properties.