The distribution of molecular gas on small scales regulates star formation and the growth of supermassive black holes in galaxy centers. Yet, the role of active galactic nuclei (AGN) feedback in shaping this distribution remains poorly constrained. We investigate how AGNs influence the small-scale structure of molecular gas in galaxy centers by measuring the clumpiness of CO(3 − 2) emission observed with the Atacama Large Millimeter/submillimeter Array (ALMA) in the nuclear regions (50 − 200 pc from the AGNs) of 16 nearby Seyfert galaxies from the Galaxy Activity, Torus, and Outflow Survey (GATOS). To quantify clumpiness we applied three different methods: (1) the median of the pixel-by-pixel contrast between the original and smoothed maps; (2) the ratio of the total excess flux to the total flux, after subtracting the background smoothed emission; and (3) the fraction of total flux coming from clumpy regions, interpreted as the mass fraction in clumps. We find a negative correlation between molecular gas clumpiness and AGN X-ray luminosity (LX), suggesting that higher AGN activity is associated with smoother gas distributions. All methods reveal a turnover in this relation around LX = 1042 erg s−1, possibly indicating a threshold above which AGN feedback becomes efficient at dispersing dense molecular structures and suppressing future star formation. Our findings provide new observational evidence that AGN feedback can smooth out dense gas structures in galaxy centers.