Within coastal nurseries, the distribution of juvenile flatfish may depend on small-scale habitat variability. The presence of ecosystem engineers is known to have important impacts in coastal sediments. Lanice conchilega is a well-known marine ecosystem engineer of shallow soft bottom ecosystems, shaping the macrobenthic community and attracting flatfish. The present study examines the relation between juvenile flatfish and L conchilega reefs through two experiments. In a field experiment in the Dutch part of the North Sea, the benthic habitat is evaluated by comparing relative differences in numbers of juvenile flatfish between ecosystem engineered habitats and adjacent bare sand (i.e. non-ecosystem engineered) habitats. The hypothetical shelter seeking behaviour was further examined using stomach content analyses. Results show that juvenile plaice Pleuronectes platessa was the dominant species within the tube worm habitat and the species selects specifically for this biogenic habitat. This selection was explained as feeding behaviour. In a complementary laboratory study, food was excluded and the shelter function of the ecosystem engineered habitat was investigated. This experiment quantifies the selection for this habitat by juveniles of the common sole Solea solea. Results from the flume experiment, manipulating the number of tube worms, show that distribution of sole was not random when current velocities are high. The selected habitat is the one with low density tube worm aggregations. Overall, we conclude that structuring benthos plays an important role for juvenile flatfish, both as refuge and as feeding ground.