Carbonates are among the most ubiquitous minerals in nature and are of significant interest in the geology and materials sciences communities, but studies concerning iron carbonate (i.e., siderite) mineralization processes and morphogenesis are less well developed. In this paper, we describe an environmentally benign biomolecule-assisted hydrothermal synthesis strategy to obtain siderite spherulites. Our results show that the formation of siderite microspheres is a successive multistep growth process involving a rod→peanut→dumbbell→sphere transition, which is driven by the intrinsic electric forces of siderite crystallites. Addition of the biomolecule ascorbic acid not only prevents Fe2+ oxidation in the alkaline solution environment but also modifies the growth of siderite. Moreover, with increasing Fe2+ concentrations, siderite nanoparticles or nano-sized triangular pyramids appear one after the other on the preformed spherical surfaces, resulting in different surface textures of the siderite microspheres. The surface morphological modifications of the siderite microspheres can be attributed to the secondary nucleation and overgrowth of siderite nanocrystals. The siderite microspheres so obtained were then used as solid precursor minerals to form secondary magnetite through oxygen-limited thermolysis at 300 °C. The thermolysis experiments demonstrate the possibility that the size and morphology of secondary magnetite particles are influenced by the precursor siderite, suggesting that magnetite microcrystals with elongated or other uncommon morphologies in nature may potentially inherit the antecedent morphologies of Fe-carbonate-bearing minerals. Moreover, measurements of the magnetic properties of magnetite products after thermolysis show that the saturation magnetizations (Ms) of three kinds of magnetite microspheres are 52.5, 62.8 and 78.6 emu/g, which vary according to increasing Fe2+ concentrations used in the synthesis of the precursor siderite.