Vaccine scepticism poses a significant global health risk, which has again become clear during the ongoing Covid-19 pandemic. Previous research has identified spirituality as an important contributor to general vaccine scepticism. In the present manuscript, we assessed whether self-identified spirituality similarly contributes to scepticism towards Covid-19 vaccines, vaccine uptake, and indecisiveness in intention to be vaccinated. We conducted three studies online in the UK in late 2020, early 2021, and the summer 2021. In Studies 1 and 2 (N = 585), as expected, individuals who strongly identified as spiritual were more sceptical about Covid-19 vaccines. This association was explained by low faith in science, but not by conspiracy beliefs. Importantly, among the vaccinated participants, those who were more spiritual were more indecisive to get a Covid-19 vaccine. Using structural equation modelling (SEM), we further found that spirituality directly predicted lower likelihood of being vaccinated against Covid-19 (Study 3, N = 456). We also identified low science literacy as an additional predictor of Covid-19 scepticism, but not self-reported vaccine uptake. To conclude, spiritual beliefs are an important factor to consider when aiming to increase understanding of vaccine-related science scepticism and vaccination rejection.