This dataset contains biogeochemical, sedimentological, bio-optical and hydrographical data from the PeCaBeau (Permafrost Carbon on the Beaufort Shelf) expedition to the Beaufort Sea on CCGS Amundsen in fall 2021. The PeCaBeau project aims to track the movement and transformation of material from permafrost thaw along the land-to-ocean continuum. This multi-disciplinary effort investigates the sediment column between subsea permafrost and the seafloor, the water column, the atmosphere and the interfaces between these three components. By studying the sources, quantities and the quality of organic matter in the water column and in sediments, we aim to improve assessments of the Beaufort shelf as a carbon source or sink, and place these outcomes in the context of the Holocene paleoenvironment and transgressed permafrost. Sampling operations took place in the Southern Beaufort Sea with five major across-shelf transects. Bathymetric and subbottom mapping surveys were conducted during the entire cruise. Radiometric measurements were performed under way and at 18 locations. Water-column profiling and sediment sampling were conducted at 35 and 27 stations, respectively.