The inherent heterogeneity of carbonate rocks suggests that carbonate-hosted fault zones are also likely to be heterogeneous. Coupled with a lack of host–fault petrophysical relationships, this makes the hydraulic behaviour of carbonate-hosted fault zones difficult to predict. Here we investigate the link between host rock and fault rock porosity, permeability and texture, by presenting data from series of host rock, damage zone and fault rock samples from normally faulted, shallowly buried limestones from Malta. Core plug X-ray tomography indicates that texturally heterogeneous host rocks lead to greater variability in the porosity and permeability of fault rocks. Fault rocks derived from moderate- to high-porosity (>20%) formations experience permeability reductions of up to six orders of magnitude relative to the host; >30% of these fault rocks could act as baffles or barriers to fluid flow over production timescales. Fault rocks derived from lower-porosity (<20%) algal packstones have permeabilities that are lower than their hosts by up to three orders of magnitude, which is unlikely to impact fluid flow on production timescales. The variability of fault rock permeability is controlled by a number of factors, including the initial host rock texture and porosity, the magnitude of strain localization, and the extent of post-deformation diagenetic alteration. Fault displacement has no obvious control over fault rock permeability. The results enable better predictions of fault rock permeability in similar lithotypes and tectonic regimes. This may enable predictions of across-fault fluid flow potential when combined with data on fault zone architecture.