There has been a surge of interest in research integrity over the last decade, with a wide range of studies investigating the prevalence of questionable research practices (QRPs). However, nearly all these studies focus on research design, data collection and analysis, and hardly any empirical research has been done on the occurrence of QRPs in the context of research funding. To fill this gap, we conducted a cross-sectional pre-registered survey of applicants, reviewers and panel members from the Research Foundation–Flanders (FWO), one of the main funding agencies in Belgium. We developed a bespoke survey and further refined it through feedback from experienced researchers and a pilot study. We asked how often respondents had engaged in a series of QRPs over the last ten years. A total of 1748 emails were sent, inviting recipients to participate in the survey, complemented by featuring the survey in the FWO newsletter. This resulted in 704 complete responses. Our results indicate that such QRPs are remarkably prevalent. Of the 496 participants who answered both the applicant and reviewer track, more than 60% responded that they engaged regularly in at least one of such practices, and around 40% indicated that they engaged at least occasionally in half of the QRPs queried. Only 12% reported not to have engaged in any of the QRPs. Contrary to our hypotheses, male respondents did not self-report to engage in the QRPs more often than female respondents, nor was there an association between the prevalence of QRPs and self-reported success rate in grant funding. Furthermore, half of the respondents indicated that they doubted the reliability of the grant peer review process more often than not. These results suggest that preventive action is needed, and provide new reasons to reconsider the practice of allocating research money through grant peer review.