This study presents a new, simple way to obtain mesoporous calcite structures via a green method using an eco-friendly surface-active compound, surfactin, as a controlling agent. The effects of synthesis time and surfactin concentration were investigated. The obtained structures were characterized by X-ray powder diffraction (XRD), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC) coupled with gas mass spectrometry (QMS) analysis. The experimental data showed that surfactin molecules significantly changed the morphology of the calcite crystals, roughening and deforming the surface and creating a greater specific surface area, even at low biosurfactant concentrations (10 ppm). The size of the crystals was reduced, and the zeta potential value of calcium carbonate was more negative when more biosurfactant was added. The XRD data revealed that the biomolecules were incorporated into the crystals and slowed the transformation of vaterite into calcite. It has been shown that as long as vaterite is present in the medium, the calcite surface will be less deformed. The strong influence of surfactin molecules on the crystal growth of calcium carbonate was due to the interaction of surfactin molecules with free calcium ions in the solution as well as the biomolecules adsorption at the formed crystal surface. The role of micelles in crystal growth was examined, and the mechanism of mesoporous calcium carbonate formation was presented.