This paper focuses on the functional analysis of Swifterbant pottery (c. 5000–3800 cal BC) in the Lower Rhine-Meuse area (the Netherlands). It examines pottery use across the transition to agriculture and aims to assess temporal changes in human-animal relations during the 5th millennium BC in the Lower Rhine-Meuse area through lipid residue analysis. We conducted lipid residue analysis of 49 samples from four Swifterbant sites: Hardinxveld-Giessendam Polderweg, Hardinxveld-Giessendam De Bruin, Brandwijk-het Kerkhof, and Hazendonk. A combined approach using both GC-MS and GC-C-IRMS of residues absorbed into the ceramic was employed to identify their context. Their context was then compared to published faunal datasets to present the relative abundance of taxa detected in the lipid residues. Evidence of processing freshwater fish was found in all sites, presenting that it was a continuous and primary function of Swifterbant pottery in the Lower Rhine-Meuse area starting from its first appearance at c. 5000 cal BC till the end of 5th millennium BC regardless of vessel form, size, decoration or temper. The results of our analysis also present temporal changes in the exploitation of food resources from the early to the late 5th millennium BC. From the mid 5th millennium BC onwards, vessels were also used to process different ranges of foodstuffs such as terrestrial resources and dairy products. The identification of dairy residue is the first direct evidence so far from Swifterbant pottery. We tentatively explain these results as an indication of presence of different culinary practices that had developed through the 5th millennium in the Lower Rhine-Meuse area and that the use of Swifterbant pottery is a direct reflection of changing cultural preferences on food preparation and consumption.