In this study, the hydroxyapatite (HAp) in the form of nanoparticles was synthesized through the wet co-precipitation method and loaded with plant extract from Calendula officinalis L. rich in biologically active myo-inositol, and the 5-fluorouracil anticancer drug. The obtained nanomaterials have rod-like structures approx. 30 nm in diameter and 100 nm in length. FT-IR analysis results proved the immobilization of biologically active compounds. The loading of plant extract into the carrier improved the stability of colloidal suspension, which was confirmed with turbidimetry. The composite modified with calendula extract and drug (HAp@Cal@5-flu) effectively scavenges the DPPH radicals, with a radical scavenging activity (RSA) of about 20.0 ± 1.3%. The effect is supported by the DFT calculations of the HOMO-LUMO, presenting the chemical reactivity of the molecules loaded into the HAp. The in vitro cytotoxicity results on SKOV-3 ovarian cancer cells show the pronounced cytotoxic effect of the HAp@Cal@5-flu. The calendula extract loading into the carrier provided better interactions with the tumorous biomimetic membranes studied with a Langmuir trough, making it a promising material in nano-biomedicine, including drug delivery and targeted cancer treatment.