The present study investigated the morphology of fresh and brine-cured table olives (TOs) as well as the changes that occur when drupes are attacked by the fruit fly Bactrocera oleae. Morphological analyses were performed using light microscopy (LM) and environmental scanning electron microscopy coupled with energy dispersive spectroscopy (ESEM-EDS). The LM analysis was carried out with visible light to evaluate sections stained with either PAS or Azan mixtures as well as unstained sections observed at fluorescence microscopy. The results of the analyses showed that: i) Azan and PAS staining played a useful complementary role, increasing the information provided by the histological analysis. Indeed, in both fresh and brine-cured TOs, epidermal layers and mesocarpal cells were clearly revealed, including sclereid cells. The histological analysis allowed also to identifying the presence of secoiridoid-biophenols (seco-BPs) in both cell walls and vacuoles, as well as in the drupe regions that had been attacked by fruit flies, where they were found at higher concentrations; ii) in fresh and brine-cured olives, the excitation at 480 nm revealed the distribution of the fluorophores, among which the seco-BP are enclosed; iii) the ESEM-EDS analysis revealed the natural morphology of fresh olives, including the dimensions of their cell layers and the size and depth of the mechanical barriers of suberized or necrotic cells around the larva holes. In addition, the elemental composition of regions of interest of the drupe was determined in fresh and brine-cured TOs. The results highlighted the effectiveness of combined use of LM and ESEM-EDS in order to obtain a picture, as complete as possible, of the structural morphology of TOs. Such analytical combined approach can be used to support multidisciplinary studies aimed at the selection of new cultivars more resistant to fly attack.