The Middle Neolithic (4300–4000 cal. yr BC) archaeological sites in the Swifterbant area were typically regarded to represent a transitional phase between a hunter-gatherer and agricultural subsistence. The discovery of a tilled layer on one of the sites (S4) site in 2007 during a renewed excavation campaign (2004–2007) was made possible by a close cooperation between archaeologists, diatom specialists and micromorphologists. Intensive sampling and micromorphological investigation revealed that the Swifterbant cultural layers typically consists of micro-laminated deposits of phytoliths and charred plant remains with waste. This led to the reinterpretation of the sites as middens rather than settlements. At least five levels could be identified that had been tilled with some kind of hand-tool. These levels were separated by natural clay deposits and midden layers. These results, and reinterpretation of observations from two other sites in the Swifterbant area (S2 and S3) indicate that tillage and crop production formed a regular part of the subsistence of the inhabitants during the Middle Neolithic. Rather than a transitional phase, the sites investigated probably should be regarded as traces of a fully agricultural society.