The origin of sedimentary dolomite has become a long-standing problem in the Earth Sciences. Some carbonate minerals like ankerite have the same crystal structure as dolomite, hence their genesis may provide clues to help solving the dolomite problem. The purpose of this study was to probe whether microbial activity can be involved in the formation of ankerite. Bio-carbonation experiments associated with microbial iron reduction were performed in batch systems with various concentrations of Ca2+(0–20 mmol/L), with a marine iron-reducing bacterium Shewanella piezotolerans WP3 as the reaction mediator, and with lactate and ferrihydrite as the respective electron donor and acceptor. Our biomineralization data showed that Ca-amendments expedited microbially-mediated ferrihydrite reduction by enhancing the adhesion between WP3 cells and ferrihydrite particles. After bioreduction, siderite occurred as the principal secondary mineral in the Ca-free systems. Instead, Ca-Fe carbonates were formed when Ca2+ ions were present. The CaCO3 content of microbially-induced Ca-Fe carbonates was positively correlated with the initial Ca2+ concentration. The Ca-Fe carbonate phase produced in the 20 mmol/L Ca-amended biosystems had a chemical formula of Ca0.8Fe1.2(CO3)2, which is close to the theoretical composition of ankerite. This ankerite-like phase was nanometric in size and spherical, Ca-Fe disordered, and structurally defective. Our simulated diagenesis experiments further demonstrated that the resulting ankerite-like phase could be converted into ordered ankerite under hydrothermal conditions. We introduced the term “proto-ankerite” to define the Ca-Fe phases that possess near-ankerite stoichiometry but disordered cation arrangement. On the basis of the present study, we proposed herein that microbial activity is an important contributor to the genesis of sedimentary ankerite by providing the metastable Ca-Fe carbonate precursors.