This data is associated with a paper presenting the results of a dual approach for assessing fossil benthic foraminiferal communities using both traditional morphology-based analyses and sedimentary ancient DNA (sedaDNA) metabarcoding. The main objectives are to test the feasibility of sedaDNA analysis to assess foraminiferal biodiversity in temperate shelf sediments off a major river system through time (Le Croisic), and to point out the similarities and differences between classical and molecular methods. Our results show that in contrast to the high foraminiferal diversity obtained from classic morphological analysis (over 140 species), the sedaDNA analysis yielded only twenty Operational Taxonomic Units (OTUs), which can be considered as equivalent to species. This strongly suggests a bad preservation of foraminiferal DNA downcore, likely due to the relatively “high” temperature of the study site (14°C), and/or to a methodological bias (e.g., insufficient amount of extracted sediment). In the total sedaDNA, more than 90% of the reads were assigned to monothalamids. In contrast, only a small number of mineralized taxa—highly dominant when identified using the morphological approach—were detected. This could be due to the naturally higher abundance of monothalamids compared to hard-shelled foraminifera. While this abundance is reflected in sedaDNA, it is not preserved in fossil morphological assemblages. In addition, the sedaDNA of monothalamids might be easier to extract and their barcode to amplify than hard-shelled foraminifera. The discrepancies between the microfossil data and sedaDNA also include several species (e.g., Ammonia confertitesta (T6), Elphidium oceanense (S3), Nonionella sp. T4 and Nonionella sp. T6) that were rarely or not found in the fossil material which might be an indication of the presence of propagules, morphologically undetected in the >63µm size fraction used. Finally, the presence of sequences of Ammonia confertitesta (T6) in the deep layer of the study core suggests that this species, considered until now as recently invasive in the European coast, could have been present in the Atlantic coast several thousand of years ago, way before any anthropogenic activity involving international shipping and commercial trades.