In light of increasing calls for transparent reporting of research and prevention of detrimental research practices, we conducted a cross-sectional machine-assisted analysis of a representative sample of scientific journals’ instructions to authors (ItAs) across all disciplines. We investigated addressing of 19 topics related to transparency in reporting and research integrity. Only three topics were addressed in more than one third of ItAs: conflicts of interest, plagiarism, and the type of peer review the journal employs. Health and Life Sciences journals, journals published by medium or large publishers, and journals registered in the Directory of Open Access Journals (DOAJ) were more likely to address many of the analysed topics, while Arts & Humanities journals were least likely to do so. Despite the recent calls for transparency and integrity in research, our analysis shows that most scientific journals need to update their ItAs to align them with practices which prevent detrimental research practices and ensure transparent reporting of research.