Electrical and fluid flow properties of porous media are directly related to the morphology of pores and the connectivity of the pore network. Both are closely linked to the amount and type of intrinsic microporosity in carbonate rocks, which is not resolved by conventional techniques. Broad-ion-beam (BIB) milling produces high-quality true-two-dimensional cross sections for scanning electron microscopy (SEM) and enables accurate quantification of carbonate microporosity for the first time. The combination of BIB-SEM mosaics with optical micrographs yields a multiscale digital image analysis (MsDIA) spanning six orders of magnitude. In this paper, the pore structures of 12 different carbonate rock samples from various rock types are quantified using MsDIA. Mercury injection capillary pressure measurements are used to assess pore-throat properties. The quantified pore-structure parameters are correlated with plug measurements of electrical resistivity and permeability. Results indicate that petrophysical properties are closely linked to the type of microporosity, which is distinctive for a certain rock type. Rock types with crystalline microporosity, such as mudstone and dolomite, generally show good connectivity, in which the size of the pore-network determines if the rock favors either hydraulic or electric flow. Rock types with intercement or micromoldic microporosity, such as bindstone and travertine, show variations in connectivity due to layering and moldic micropores of biological origin. Furthermore, pore-size distributions (PSD) follow a power law in all samples, despite their depositional and diagenetic differences. The slope of the PSD correlates with the electric properties, in which samples with a steeper slope show lower cementation factors. The linearity of the power law distribution enables predictions of pore populations outside the investigated length scales.