A pluridisciplinary approach was used to define iodine immobilization mechanisms by biocarbonates in a natural marine carbonate-bearing clayey formation. For this purpose, different techniques of observation (optical microscope, scanning electron microscope (SEM), cathodoluminescence (CL)) and of analyses (infrared spectrometry (IR), electron microprobe (EPMA), spatially resolved synchrotron-based X-ray fluorescence (μ-XRF) and X-ray diffraction (μ-XRD)) were performed on two entire and centimeter-sized carbonate shells of the Callovian-Oxfordian (160 Ma) clayey formation from the ANDRA (French Radioactive Waste Management Agency) Underground Research Laboratory (Meuse/Haute Marne, France), in the Eastern part of the Paris Basin. Combined (SEM, CL, IR and μ-XRD) data indicates that the biostructure of the Rhynchonella shell is relatively well-preserved but bio-aragonite slowly transforms into calcite, whereas the bivalve shell is entirely recrystallized into diagenetic calcite and celestite. EPMA and μ-XRF data show bioaccumulation of iodine in carbonate shells, confirming previous work on present-day mollusks. EPMA analyses give evidence of iodine content up to 1200 ppm in the preserved Rhynchonella shell and up to 2000 ppm in recrystallized bivalve shell. μ-XRF elemental mapping shows that iodine is more homogeneously distributed in bio-calcite of the Rhynchonella shell than in recrystallized calcite of the bivalve shell, suggesting a loss of iodine during re-crystallization processes, but not a total exclusion of iodine from the carbonate structure. Combined EPMA data and μ-XRF elemental maps do not give evidence of any correlation between the iodine location and the distribution of other elements.