MOTIVATION: In the past decades, many statistical methods for integrating multi-omics data have been developed. They have been implemented into software tools, which differ widely in their programming choices, such as the format required for data input, or the format of the generated integration results. This lack of standards renders cumbersome and time-intensive the application and comparison of different integration tools to the same multi-omics dataset. RESULTS: We have developed the moiraine R package for constructing reproducible multi-omics integration pipelines, which enables users to apply one or more statistical methods for multi-omics integration to their own multi-omics dataset. moiraine facilitates the preprocessing of the omics datasets and automates their formatting for the integration step. It simplifies the interpretation and evaluation of the integration results through the construction of visualizations in which metadata about samples and features can easily be included. Crucially, it enables the comparison of results obtained with different integration tools, allowing users to assess the robustness of their results. AVAILABILITY AND IMPLEMENTATION: The moiraine R package is publicly available at https://github.com/Plant-Food-Research-Open/moiraine; an archival snapshot of the package is available on Zenodo at https://doi.org/10.5281/zenodo.17172718. A detailed tutorial is available at https://plant-food-research-open.github.io/moiraine-manual/.