X-ray micro-computed tomography (micro-CT) is a widely used tool to non-destructively observe the internal structure of objects. Synchrotron Radiation X-ray micro-CT uses X-ray produced by acceleration of electrons to achieve higher spatial resolution is lower acquisition time. Parasitic Platyhelminthes belonging to the Trematoda class encompass a diverse range of species that cause diseases in both humans and animals. In parasitological investigations, the intra-molluscan developmental stage of Trematoda has remained a challenging black box, often requiring destructive methods for its observation. A in-vivo follow-up of the intramolluscan development stages would offer the opportunity to evaluate factors that promote or impede parasite development. Here, we explore the potential of SRμCT to provide valuable insights into this stage while keeping the sample intact. To reach toward in-vivo scanning, this study delves into mollusc anaesthesia, contrast agent selection for preliminary micro-CT tests and SRμCT scans, and their application for parasitological investigations in snail host Ampullaceana balthica. Listerine 20% was selected as an optimal anaesthetic; however, it was found ineffective during live SRμCT scans. In-vivo and fixed contrast agent experiments underscored the delicate balance between efficacy and potential harm, with Phosphotungstic Acid (PTA) showing promise. Contrarily to live scans which resulted in motion-blurred images, the high-quality scans conducted on preserved specimens allowed for the quantification and 3D reconstruction of parasite infections without causing any damage to the samples, marking it the first study utilizing this technique on trematode parasites in their first intermediate host. Beyond technical achievements, our work has broader ecological implications, providing a promising avenue for studying parasites' roles in ecosystems. This methodology’s potential to calculate infection ratios non-destructively offers a novel approach to understanding parasite biomass dynamics in food webs.