Templated assembly of organic molecules constitutes a promising approach for fabricating functional nanostructures at surfaces with molecular-scale control. Using the substrate template for steering the adsorbate growth enables creating a rich variety of molecular structures by tuning the subtle balance of intermolecular and molecule–surface interactions. On insulating surfaces, however, surface templating is largely absent due to the comparatively weak molecule–surface interactions compared to metallic substrates. Here, we demonstrate the activation of substrate templating in molecular self-assembly on a bulk insulator by controlled deprotonation of the adsorbed molecules upon annealing. Upon deposition of 4-iodobenzoic acid onto the natural cleavage plane of calcite held at room temperature, high molecular mobility is observed, indicating a small diffusion barrier. Molecular islands only nucleate at step edges. These islands show no commensurability with the underlying substrate, clearly indicating the absence of surface templating. Upon annealing the substrate, the molecules undergo a transition from the protonated to the deprotonated state. In the deprotonated state, the molecules adopt a well-defined adsorption position, resulting in a distinctly different, substrate-templated molecular structure that is stable at room temperature. Our work, thus, demonstrates the controlled activation of substrate templating by changing the molecule–surface interaction upon annealing.