Abstract The soft excess is a significant emission component in the soft (<1 keV) X-ray spectra of many active galactic nuclei (AGN). It has been explained by disk reflection, a warm corona, and other models. Understanding its origin is crucial for the energy budget of AGN emission, and for using it to study the inner accretion disk. Here, we track the weeks-to-months variability of several AGN that show different levels of soft excess strength with NICER. We use the variability timescales to compare the relative size of the soft excess emission region to the corona producing the hard X-ray emission above 1 keV. We find that the size of the soft excess emission region relative to the corona is not the same for the three sources studied. For TON S180, the soft excess region is comparable in size to the hard corona. While for MRK 335 and 1H0707-495, the soft excess region is larger than the corona by a factor of 2–4. This is the first time the relative sizes are quantified independently of the assumptions of the spectral models.