Through the process of biomineralization living organisms use macromolecules to direct nucleation and growth of nanophases of a variety of inorganic materials. Evidence shows this is a widespread strategy for controlling the timing, polymorphism, morphology, and crystallographic orientation of CaCO3 nuclei. In the past decade, self-assembled monolayers (SAMs) of alkanethiols have been used as a simple model to reproduce the controls of organic substrates. However, despite the importance of nucleation phenomena in the crystallization of inorganic materials our understanding of the reaction dynamics is extremely limited because, until recently, there was no experimental tool that possessed the spatial and temporal resolution needed to capture the formative events in the process. Issues such as the formation of amorphous precursors, and polymorph selection during the initial stages of nucleation, as well as the structural relationships and energetic controls of the inorganic matrix on the emerging nucleus have not been fully explored. To address these gaps in our understanding we have developed a suite of in situ methods and applied them, along with synchrotron-based X-ray spectroscopies, to CaCO3 nucleation. We used these methods to observe CaCO3 nucleation rates on alkanethiol SAMs. We found that for two carboxyl-terminated alkanethiol SAMs with odd (mercaptoundecanoic acid) and even (mercaptohexadecanoic acid) carbon chains, the effective interfacial energy is reduced from about 109 mJ m−2 in solution to 81 mJ m−2 and 72 mJ m−2, respectively, showing that templating is driven by a reduction in the thermodynamic barrier to nucleation. We also report in situ transmission electron microscopy (TEM) observations of crystal nucleation and growth in solution at the nanometre scale and video rates. This capability is enabled by the combination of a custom designed TEM stage and fluid cell. Significantly, the design of the cell and holder ensures temperature and electrochemical control over the reaction environment, allowing for direct investigation of nucleation. Our first results show that CaCO3 nucleates via nanoparticles of an apparent metastable precursor— most likely ACC—followed by consolidation and faceting. Finally, we report insights from the use of synchrotron-based near-edge X-ray absorption fine structure spectroscopy (NEXAFS) into the evolution of the SAM during the nucleation process. Based on measurements of SAM monomer orientation, we argue that the ability of the SAM to reorganize during the nucleation process is a key feature of an organic matrix that successfully directs mineralization.