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JWST has revealed an abundance of low-luminosity active galactic nuclei (AGN) at high redshifts (z > 3), pushing the limits of black hole (BH) science in the early Universe. Results have claimed that these BHs are significantly more massive than expected from the BH mass–host galaxy stellar mass relation derived from the local Universe. We present a comprehensive census of the BH populations in the early Universe through a detailed stacking analysis of galaxy populations, binned by luminosity and redshift, using JWST spectroscopy from the CEERS, JADES, RUBIES, and GLASS extragalactic deep field surveys. Broad Hα detections in 31% of the stacked spectra (5/16 bins) imply median BH masses of 105.16–106.08 M⊙, and the stacked spectral energy distributions of these bins indicate median stellar masses of 107.84–108.56 M⊙. This suggests that the median galaxy hosts a BH that is at most a factor of 10 times overmassive compared to its host galaxy, and lies closer to the locally derived MBH–M* relation. We investigate the seeding properties of the inferred BHs and find that they can be well explained by light stellar-remnant seeds undergoing moderate Eddington accretion. Our results indicate that individual detections of AGN are more likely to sample the upper envelope of the MBH–M* distribution, while stacking of “normal” galaxies and searching for AGN signatures can overcome the selection bias of individual detections.