Tropical corals rely on their algal symbionts (Symbiodiniaceae) for nutrition and survival, but this partnership is increasingly threatened by global warming. Understanding the molecular interaction between corals and their algal symbionts and the mechanism of coral climate resilience are crucial for developing novel coral conservation strategies. While many studies have examined molecular interactions in the coral-algal symbiosis, major knowledge gaps remain as traditionally whole tissue homogenates have been used for analysis. Homogenisation removes the spatial context of the intricate coral-algal association, making it challenging to determine the tissue origin of a molecule and interpret its function, particularly at the symbiont–host interface. Here, we present a spatial metabolomics imaging workflow that overcomes the challenge of cryosectioning scleractinian corals and reveals coral and algal symbiont metabolites in situ at a spatial resolution of 5 µm. Using this novel method, we have successfully separated the metabolome of different cellular layers (e.g., epidermis, gastrodermis) in situ. This presentation will cover methods for sample preparation and annotation, as well as results showing improved coverage of the metabolites detected with mass spectrometry imaging (MALDI-MSI). By enhancing the resolution of spatial metabolomics, our approach will advance knowledge on coral-algal metabolic interactions.