Calcium carbonate (CaCO3) is one of the most significant biominerals in nature. Living organisms are able to control its biomineralization by means of an organic matrix to tailor a myriad of hybrid functional materials. The soluble organic components are often proteins rich in acidic amino-acids such as l-aspartic acid. While several studies have demonstrated the influence of amino acids on the crystallization of calcium carbonate, nanoscopic insight of their impact on CaCO3 mineralization, in particular at the early stages, is still lacking. Herein, we implement liquid phase-transmission electron microscopy (LP-TEM) in order to visualize in real-time and at the nanoscale the prenucleation stages of CaCO3 formation. We observe that l-aspartic acid favors the formation of individual and aggregated prenucleation clusters which are found stable for several minutes before the transformation into amorphous nanoparticles. Combination with hyperpolarized solid state nuclear magnetic resonance (DNP NMR) and density functional theory (DFT) calculations allow shedding light on the underlying mechanism at the prenucleation stage. The promoting nature of l-aspartic acid with respect to prenucleation clusters is explained by specific interactions with both Ca2+ and carbonates and the stabilization of the Ca2+-CO32-/HCO3- ion pairs favoring the formation and stabilization of the CaCO3 transient precursors. The study of prenucleation stages of mineral formation by the combination of in situ LP-TEM, advanced analytical techniques (including hyperpolarized solid-state NMR), and numerical modeling allows the real-time monitoring of prenucleation species formation and evolution and the comprehension of their relative stability.