Manganese (Mn) is an essential element that intervenes in several plant metabolic processes. The olive tree, and its fruits and leaves, are known as a source of nutraceuticals since they are rich in biophenols. However, there is still a serious lack of data about biophenolic distribution in olive stems and roots under Mn fertilisation. In this context, our study aimed to examine the effects of Mn fertilisation on the biophenolic profile in the leaves, stems, and roots of the ‘Istarska bjelica’ olive cultivar. The experiment was set up in a greenhouse, during a period of five months, as a random block design consisting of three treatments with varying Mn concentrations in full-strength Hoagland’s nutrient solution (0.2 µM Mn, 12 µM Mn, and 24 µM Mn). The obtained results indicate that the amount of Mn in the examined olive plant tissues was significantly higher under 12 µM Mn and 24 µM Mn treatments compared to that of the 0.2 µM Mn treatment. While the concentration of biophenols varied in roots depending on the compound in question, a strong positive impact of the increased Mn concentration in nutrient solution (12 µM Mn and 24 µM Mn) on the concentrations of the main biophenolic compounds was observed in stems. The concentration of oleuropein in leaves almost doubled at 24 µM Mn, with the highest Mn concentration, as compared to the 0.2 µM Mn treatment. The obtained results led to the conclusion that the supply of Mn could enhance the concentration of some biologically active compounds in olives grown hydroponically, implying a critical need for further investigation of Mn fertilisation practices in the conventional olive farming system.