Previous studies have demonstrated links between greater religiosity and lower COVID-19 vaccination rates. This article delves into an explanation for these relationships by investigating the role of belief in science and moral foundations that may elucidate why belief in God is associated with lower vaccination intention. Study 1 (n = 689), comparing Polish Catholics and atheists, revealed that Catholics exhibited a lower COVID-19 vaccination intention, and this relationship is mediated by a lower belief in science among Catholics. Furthermore, as identification with a denominational group increased, the negative correlation between being Catholic and belief in science intensified. Findings from Study 2, conducted among Catholics (n = 752), indicated that intrinsic religious orientation is negatively related to COVID-19 vaccination intention, and this relationship is fully mediated by belief in science. Conversely, extrinsic religious orientation was positively linked to COVID-19 vaccination intention. Study 3 (n = 469) found that the lower vaccination intention of Catholics, compared to atheists, may be attributed to higher levels of purity and loyalty moral foundations among Catholics, which, in turn, were associated with a weaker vaccination intention. These results underscore the complex religious mechanisms within Catholics that shape their motivation to vaccinate.