Sponges are ancient metazoans that form intimate symbiotic interactions with complex microbial communities. However, the molecular mechanisms underlying these associations remain largely unknown. Metagenomic analyses has revealed a higher abundance of genes encoding eukaryotic-like proteins (ELPs) in sponge symbiotic bacteria when compared to free-living bacteria. ELPs are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. They have been postulated to be key molecular mediators of host-microbiome interactions. Our previous research identified SSA4, an ELP with ankyrin repeat domains encoded by a symbiotic gammaproteobacterium in the sponge Cymbastela concentrica. SSA4 modulates amoebal phagocytosis and interacts with a specific sponge-produced lectin protein in vitro. Here, we optimized a correlative light and electron microscopy (CLEM) method to visualize SSA4 within specific bacteria hosted in the tissue of sponge C. concentrica and its co-localization patterns with the sponge lectin protein. We enhanced both Fluorescence in situ hybridization (FISH)-CLEM and immunofluorescence-CLEM techniques, with respect to ultrathin microtomy preparation, probe hybridization, immunofluorescence labelling and image acquisition, improving fluorescent signal strength and detection sensitivity. Additionally, we established a 3D reconstruction of SSA4 and sponge lectin protein binding patterns. This optimized CLEM technique enables the visualization of protein-protein interactions within the spatial context of bacteria-host associations, providing new insights into the molecular mechanisms of sponge-bacteria symbiosis.