Cedrus atlantica is a tree species present in the south of France which, in the context of climate change, could become a conservation priority in the coming years. This tree species is also of considerable ecological and socio-economic interest in the Mediterranean Basin area, where it is mainly recognized for its durable timber, and also for the potentially interesting chemical properties of its essential oil. Studies of its heartwood formation process and the properties of its extractive compounds are therefore of interest, although very few have been conducted so far. The radial distribution of water/acetone extractives within the Atlas cedar tree (bark, sapwood, transition wood, outer heartwood and inner heartwood) selected for this study was screened at different tree height levels. High-performance liquid chromatography (HPLC) analyses were performed, especially to characterize flavonoid compounds in these extractive fractions. The radial variation of the extractive composition obtained highlights the phenomenon of heartwood formation. Assumptions were put forward as to the metabolic pathways involved in the heartwood formation process of cedar wood, based in particular on the occurrence and radial evolution of (-)-catechin, (+)-taxifolin and flavan compounds. The fungicidal and termite-repellent activities of the extracts were then tested. The water/acetone extractives from the Cedrus atlantica individual studied showed strong termite repellent activity and moderate antifungal activity against crop and fruit pathogens. Even though the sampling in this study was limited to a single tree, the results point to a potential for commercial use of Atlas cedar extractives as wood preservatives and/or as biocontrol products against pathogens of ligneous agricultural crops. Additional tests and chemical analyses will be carried out to confirm these interesting preliminary results.