Annona cherimola fruit, known as cherimoya or custard apple, is an exotic fruit from South America but is strongly produced in Andalusia, Spain. Its by-products (seeds and peel) are recognised as important sources of antioxidants, including phenolic acids, flavonoids and procyanidins. Therefore, the aim of this study was to carry out the characterization of its phenolic composition and to in vitro evaluate the bioactivity of custard apple seed and peel. Therefore, high performance liquid chromatography coupled to mass spectrometry (HPLC-ESI-qTOF-MS) was performed in order to tentatively identify their phenolic composition. In the end, 19 compounds were identified and quantified, some of them for the first time in the custard apple matrix. Then, seed and peel total phenolic content, as well as antioxidant properties, radical scavenging capacity (O2, NO, HOCl) and inhibition of enzymes involved in different pathologies (hyaluronidase, elastase, collagenase, tyrosinase, acetylcholinesterase and xanthine oxidase), were evaluated. Although both extracts showed almost similar antioxidant capacities, custard apple seed stood out slightly more than peel (171 ± 2 vs. 130.0 ± 0.4 μmol TE/g DE, resp.), especially as ·NO scavenger (IC50 1.5 ± 0.2 vs. 11.8 ± 0.3 mg/L, resp.) and hyaluronidase inhibitor (IC50 170 ± 10 vs. 460 ± 20mg/L, resp.). Finally, the application of extracts on a real human model of platelet aggregation was performed, reporting antiaggregatory effects in agonist-promoted platelet thrombus formation. All these results show that custard apple by-products are stated as interesting sources of bioactive compounds with multiple industrial applications for the development of high-added-value products, such as functional foods, nutraceuticals and cosmeceuticals, promoting the circular bioeconomy of these by-products.