Aluminum coatings, which are applied by physical vapor deposition (PVD), have to be virtually defect-free in barrier applications for the packaging industry. When aluminum is applied to paper, hygroexpansion and substrate roughness can impair the aluminum coating. Neither effect is easy to detect by microscopy, but both can manifest as an increase in electrical resistance. Here, we quantified the effect of substrate paper hygroexpansion and surface roughness on the effective resistivity ρEFF of aluminum coatings. The sheet resistance of aluminum coated onto four different rough paper surfaces was measured via eddy currents at different relative humidity (0%–95%). The mass of aluminum per unit area was determined by inductively-coupled plasma mass spectrometry (ICP–MS). We calculated ρEFF based on the measured resistance and aluminum mass per unit area, combined with a value for aluminum density from the literature. The substrate roughness was proportional to ρEFF. Relative humidity correlated with the moisture content of the paper substrate according to the Guggenheim, Anderson, and De Boer (GAB) equation, whereas the moisture content showed a linear correlation with hygroexpansion. At relative humidity of up to 50%, hygroexpansion was linearly correlated with the increase in ρEFF, which is related to the mechanical straining and deformation of aluminum. At higher humidity, aluminum started to crack first on rough substrates and later on smooth substrates. The increase in ρEFF was larger on rough substrates. The findings highlight the need for information about substrate roughness, humidity, and hygroexpansion when eddy current measurement results are compared, and will help to ensure that aluminum coatings, applied by PVD, are defect-free.