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Abstract Ferromanganese concretions commonly occur in shallow‐water coastal regions worldwide. In the Baltic Sea, they can record information about past and present underwater environments and could be a potential source for critical raw materials. We report on their microstructural characteristics and magnetic properties and link them to their formation mechanisms and environmental significance. Microstructural investigations from nano‐ and micro‐computed tomography, electron microscopy, and micro‐X‐ray fluorescence elemental mapping reveal diverse growth patterns within concretions of different morphologies. Alternating Fe‐ and Mn‐rich growth bands indicate fluctuating redox conditions during formation. Bullet‐shaped magnetofossils, produced by magnetotactic bacteria, are present, which suggests the influence of bacterial activity on concretion formation. Spheroidal concretions, which occur in deeper and more tranquil environments, have enhanced microbial biomineralization and magnetofossil preservation. Conversely, crusts and discoidal concretions from shallower and more energetic environments contain fewer magnetofossils and have a greater detrital content. Our results provide insights into concretion formation mechanisms and highlight the importance of diagenetic processes, oxygen availability, and bacterial activity in the Baltic Sea.