The biomineralization of magnetotactic bacterial magnetite nanoparticles is a topic of intense research due to the particles’ narrow size distribution and magnetic properties. Incorporation of foreign metal ions into the crystal matrix of magnetotactic bacterial magnetite has been previously examined by a number of investigators. In this study, cells of a magnetotactic bacterium, Magnetospirillum gryphiswaldense strain MSR-1 were grown in the presence of manganese, ruthenium, zinc and vanadium, of which only manganese was incorporated within the magnetosome magnetite crystals. We demonstrate that the magnetic properties of magnetite crystals of magnetotactic bacteria can be significantly altered by the incorporation of metal ions, other than iron, in the crystal structure. The Verwey transition serves as a unique marker to probe the incorporation of the dopant within the magnetosome: manganese incorporation into the magnetite nanocrystals is signaled by a suppression of the Verwey transition, as well as by changes in the crystalline structure and chemical composition of magnetosome magnetite.