Survival after transplantation of mussel seeds is crucial for the production output of blue mussels (Mytilus edulis L.) in bottom cultures. Hence, an understanding of the interactions between bed formation, habitat structure and performance of mussel seed of different origins can contribute to an optimization of the production. The effect of substrate composition and timing of formation of a mussel bed in relation to aggregation and attachment of mussels were investigated with mussel seeds obtained from two different sources: mussel seed dredged from a natural mussel bed and mussel seed collected from a suspended long line culture. The mussels were applied to experimental units of complex and smooth substrate on the sea bed. Data on aggregation (day 0, day 1 and day 2), attachment strength (day 2 and 30), loss (day 2 and 30) and growth (day 0–30) of mussels were collected during the experiment. The results showed that complex substrate indeed had a stabilizing effect on the mussel structure resulting in less aggregation and increased attachment strength. The 3D matrix forming a mussel bed was achieved faster on complex substrate, and led to reduced mortality of transplanted mussels. Despite significantly lower specific growth rates on the complex substrate, the total biomass of mussels was significantly higher on complex substrate compared to on smooth substrate due to the higher survival of mussels. Furthermore, suspended mussels aggregated more and faster and had a stronger and more rapid attachment as compared to bottom mussels. Consequently, it was concluded that when transplanting mussels, seeding with substrate increases surface complexity on the seabed and increases survival of the mussels.