Terebratulide brachiopod shells have a thin, hard outer nanocrystalline calcite layer and a hybrid fibre composite inner layer with CaCO3 fibres embedded in an organic matrix. Here we report our observation by transmission electron microscopy (TEM) of a large compartment filled with amorphous calcium carbonate (ACC) in the shell of the modern brachiopod Megerlia truncata. The compartment has the typical shape and size of fibrous calcite crystals composing the inorganic component of the hybrid fibre composite secondary shell layer. The ACC compartment is adjacent to an inclusion of foreign material that is entirely incorporated into the shell. It has most probably been produced in the course of shell reparation. Under TEM imaging conditions the amorphous carbonate crystallized in situ to vaterite and calcite. The distribution pattern of the organic component of the shell material is spatially differentiated. While in the outer, nanocrystalline primary shell layer we do not observe any organic material between the crystallites by TEM, the CaCO3 fibres of the secondary layer are surrounded by an organic sheath. In the innermost segment of the secondary layer, in addition to the organic sheaths, thick organic membranes are present. The compartment containing ACC is located between two, 1–2 μm thick, organic membranes. Our observations indicate that brachiopod shell formation may occur via an ACC precursor that is produced in an initial stage prior to the crystallization of calcite.