Diagenesis is a major control on the distribution of porosity and permeability in carbonate rocks, and therefore impacts fluid flow in the subsurface. While changes in porosity can be directly related to diagenetic petrographic characteristics such as cement distribution and dissolution features, quantifying how these textures relate to attendant changes in permeability is more challenging. Here, we demonstrate for the first time how pore-scale models, representing typical carbonate sediments and their diagenetic histories, can be used to quantify the evolution of petrophysical properties in carbonate rocks. We generate 3D pore architecture models (i.e. the spatial distribution of solid and pores) from 2D binarized images, representing the typical textural changes of carbonate sediments following hypothetical diagenetic pathways. For each 3D rock model, we extract the pore system and convert this into a network representation that allows flow properties to be calculated. The resulting porosity and permeability evolution scenarios display several ‘diagenetic tipping points’ where the decrease in permeability is dramatically larger than expected for the associated decrease in porosity. The effects of diagenesis also alter the capillary entry pressures and relative permeabilities of the synthetic cases, providing trends that can be applied to real rocks. Indeed, values of porosity and absolute permeability derived from these synthetic 3D rock models are within the range of values measured from nature. Such diagenetic pathway models can be used to provide constraints on predicted flow behaviour during burial and/or uplift scenarios using ‘diagenetic back-stripping’ of real carbonate rocks.