Ciliary beat frequency and cilia coverage are key parameters of the maturation and function of airway epithelia. In our study "In vitro platform to model the function of ionocytes in the human airway epithelium" we have reported the differentiation of airway epithelia from human induced pluripotent stem cell (hiPSCs) with similar properties to those derived from primary cells. We have used this platform to study the effect of the KO of FOXI1 and, as a consequence, the depletion of ionocytes on the function of the airway epithelium. Cilia motility and coverage were among the assessed parameters. This dataset includes ciliary beating frequency and cilia coverage data of hiPSC-AECs obtained from up to 20 high-speed microscopy videos per biological replicate using a Fourier transform method described in Fradique, Causa et al., 2023, Royal Society Open Science (https://doi.org/10.1098/rsos.230185).