The effect of a soft layer on the cone resistance of a sand layer has been studied extensively, but the same cannot be said for the case of multi-layered deposits with many (thin) alternating soil layers. For geotechnical analyses based on cone penetration test data it is difficult to estimate a representative value of the cone resistance when encountering alternating thin layers of clay or peat and sand. This paper presents physical modelling tests to understand the ‘value’ of the cone resistance in thinly multi-layered soil deposits. The test results are compared with existing analytical methods. It is concluded that the characteristic resistance of the individual layers, the layer thicknesses relative to the cone diameter and the number of layers within the zone of influence of the cone affect the cone resistance in deposits containing multiple thin soil layers. Suggestions for practical implementation are also given.