A novel inorganic consolidant has recently been proposed for the treatment of carbonate stones used in architectural and cultural heritage. The consolidant is an aqueous solution of diammonium hydrogen phosphate (DAP), which penetrates inside the stone and reacts with calcite to form hydroxyapatite (HAP). This HAP-based treatment seems very promising in several respects. It is effective in enhancing mechanical properties, only slightly alters stone transport properties, causes limited color change, and involves the use of non-toxic water solvent. However, several different treatment conditions and application methods have been investigated so far in the literature and the most suitable procedure for application in situ has not been identified yet. Therefore, in this paper a systematic investigation of the effects of different application methods of the DAP solution (brushing, poultice and immersion) was carried out. After DAP application, a further step consisting in a limewater-saturated poultice, aimed at overcoming possible issues connected to the presence of unreacted DAP in the treated stone, was performed and an “application cycle” was finally proposed. The treatments were tested on artificially weathered samples of Globigerina limestone (“Franka” type), a highly porous stone typically used in historical architecture in Malta and severely affected by decay processes. Even if Globigerina limestone is usually subject to salt-induced damage in the field, in this study artificial weathering was performed by heating to induce a controlled and uniformly distributed decay in the samples, as the presence of soluble salts would have interfered with the mechanisms of penetration and distribution of the DAP solution in the substrate, which was the main research objective. The outcome of the different treatments was evaluated in terms of consolidant penetration depth, mechanical properties, microstructure, contact angle, water sorptivity and color change, with respect to the untreated samples. The newly formed phases were characterized by SEM/EDS, FT-IR and ion chromatography. Based on the results of the study, brushing seems to be the most suitable method for DAP application, as it induces significant mechanical improvement but still limited microstructural, physical and chromatic alterations. Moreover, the benefits deriving from a higher consolidant absorption, as achieved by poultice and immersion applications (which are however much more laborious on site) are not so great in terms of HAP distribution in the substrate and consolidating performances.