Traditionally, protection of the coastal area from flooding is approached from an engineering perspective. This approach has often resulted in negative or unforeseen impacts on local ecology and is even known to impact surrounding ecosystems on larger scales. In this paper, the utilization of ecosystem engineering species for achieving civil-engineering objectives or the facilitation of multiple use of limited space in coastal protection is focused upon, either by using ecosystem engineering species that trap sediment and damp waves (oyster beds, mussel beds, willow floodplains and marram grass), or by adjusting hard substrates to enhance ecological functioning. Translating desired coastal protection functionality into designs that make use of the capability of appropriate ecosystem engineering species is, however, hampered by lack of a generic framework to decide which ecosystem engineering species or what type of hard-substrate adaptations may be used where and when. In this paper we review successful implementation of ecosystem engineering species in coastal protection for a sandy shore and propose a framework to select the appropriate measures based on the spatial and temporal scale of coastal protection, resulting in a dynamic interaction between engineering and ecology. Modeling and monitoring the bio-physical interactions is needed, as it allows to upscale successful implementations and predict otherwise unforeseen impacts.