Magnetotactic multicellular aggregates consist of several bacteria that produce iron sulfide magnetosomes through a complex and poorly understood process. We observed new amorphous mineral particles within the cytoplasm of magnetotactic multicellular aggregates. Elemental mapping and electron energy loss spectroscopy detected iron and oxygen, but not sulfur, in these particles. These amorphous particles were about the same size as mature magnetosomes, around 50-70 nm in diameter. No membranes were observed surrounding the amorphous minerals. Partially crystalline inclusions composed of a crystalline core and an amorphous region around them similar in texture to the amorphous particles were also present. The shape of these amorphous regions followed the shape of the crystalline cores they enveloped. These regions also contained oxygen and iron. The crystalline phase, as previously reported, contained sulfur and iron. The presence of independent amorphous particles has not been reported before in magnetotactic multicellular aggregates.