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 by micro-computed tomography. In the case of the olive fruit fly (Bactrocera oleae), a complete reconstruction of the galleries was obtained. The galleries were colour-coded according to the internal lumen, corresponding to the size of the larval instars. In the case of the olive moth (Prays oleae), it was confirmed that the larvae only consume olive stones, leaving the pulp tissue intact. This study revealed the evolutionary defensive adaptation that the larva has developed by making the 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 a fungal infection transmitted by the midge (Lasioptera berlesiana), microtomography revealed the infection cavity, delimited by a protective layer of tissue produced by the plant to isolate the infection zone, full of fungal hyphae and the reproductive organs of the fungus. Below and near the single external orifice present in the concave necrotic depression, two ovoid cavities were observed. These results were interpreted as successive ovipositions of B. oleae and its parasitoid L. berlesiana. High-resolution 3D rendered images are included as well as supplementary videos that could be a useful tool for future research and a valuable teaching aid.