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Abstract A complete three-dimensional reconstruction of the internal damage (oviposition holes, entry and exit galleries, cavities caused by fungal infection) of three destructive pests of olive fruit was obtained using micro-computed tomography. In the case of the olive fruit fly (Bactrocera oleae), complete reconstruction of the galleries was achieved. The galleries were colour-coded according to the size of the internal lumens produced by larval instars. In the case of the olive moth (Prays oleae), we confirmed that the larvae only consume olive stones, leaving pulp tissue intact. This study revealed the evolutionary defensive adaptation developed by larvae, creating entrance/exit gallery in the form of a zigzag with alternating angles to avoid the action of possible parasitoids. In the case of olive fruit rot, caused by fungal infection transmitted by the midge (Lasioptera berlesiana), microtomography revealed the infection cavity, which was delimited by a protective layer of tissue produced by the plant to isolate the infection zone, which contained fungal hyphae and reproductive organs of the fungus. Two ovoid cavities were observed below a single external orifice in the concave necrotic depression. These results were interpreted as successive ovipositions of B. oleae, followed by the parasitoid L. berlesiana. High-resolution 3D rendered images are included as well as supplementary videos that could be useful tools for future research and teaching aids.