We consider cosmological models based on the spectral action formulation of (modified) gravity. We analyze the coupled effects, in this model, of the presence of nontrivial cosmic topology and of fractality in the large scale structure of spacetime. We show that the topology constrains the possible fractal structures, and in turn the correction terms to the spectral action due to fractality distinguish the various cosmic topology candidates, with effects detectable in a slow-roll inflation scenario, through the power spectra of the scalar and tensor fluctuations. We also discuss explicit effects of the presence of fractal structures on the gravitational waves equations.