Diagenesis of carbonate minerals is ubiquitous throughout the geologic record. Alteration is initiated immediately after deposition, or takes place in the endo- and exoskeletons as early as during the lifetime of a given carbonate-secreting biota, and can continue throughout the burial history of carbonate sediments and rocks. Variations in the diagenetic response of carbonate archives pose challenges for the reconstruction of past environmental conditions based on proxy data. This paper comparatively assesses alteration features of different aragonitic materials by experimentally-induced diagenesis. A multitude of factors lead to different reactivity and responses of a given aragonite archive, and provide insight to the interpretation of diagenetically altered material in the rock record. Chosen materials used in this study include relatively organic-rich samples such as coral skeletons and bivalve shells, and organic-lean abiotic carbonates such as speleothems and aragonite single crystals. Obtained datasets include distributions of elements, organics, carbon and oxygen isotope ratios, and crystallographic features. Observed variations in diagenetic responses include mineralogy of the diagenetic phases, rate and extent of mineral transformation, distribution of foreign ions in the crystal lattice (primarily Sr, Mg, and S), and the number of specific processes and products along diagenetic pathways. Alteration is shown to be primarily controlled by the initial diagenetic susceptibility of the sample (including porosimetry and structural characteristics, concentrations of organic material, and primary amounts of trace elements in the carbonate, such as Mg). Structural characteristics lead to initial internally “fluid-” or “rock-buffered” conditions, with low porosity and permeability resulting in a greater effect of internal fluids and organics. Differences in the amount of organic content and internal fluids affect transformation rates, secondary mineralogy, and isotope equilibria. Samples with relatively high porosity, high mineral transformation rates, and high primary Mg/Ca, may preferentially form secondary aragonite during fast equilibration with the diagenetic environment. Our results suggest that the degree and nature of diagenetic alteration of aragonite materials are strongly controlled by the micro- to nano-scale internal architecture governing the availability and transfer of aqueous fluids. Results of this study provide significant implications for the interpretation of diagenetic signals in carbonate archives, and have direct significance for the mechanistic understanding of carbonate diagenesis and (paleo)environmental conditions.