Habitat complexity (HC) promotes species richness and abundance. Aquatic environments are faced with intense pressures that threaten the 3D structure of the seafloor, with cascading effects on ecosystem functioning and biodiversity. Maerl or rhodolith beds are marine biogenic habitats created by few species of free‐living non‐geniculate coralline algae that aggregate and form complex structures. Although their high biodiversity has been attributed to the HC provided by coralline algal nodules, the mechanisms through which HC modification affect associated communities remains uncertain in face of numerous confounding factors. Hence, we tested how changes in the extent and nature of maerl complexity drive changes in biodiversity. Using long‐term monitoring data from ten maerl beds in Brittany (France) over 12 years, we investigated the links between structural complexity, environmental conditions and benthic macrofaunal communities. HC was quantified at the coralline algal nodule and bed level, through morphometrics and density, and its effects on local diversity and on communities spatial and temporal variability were evaluated. HC promoted species richness and density of most taxa regardless of other environmental factors. These relationships were linear and no limiting threshold of complexity was found at a regional scale. HC played a more important role in driving regional diversity patterns than other measured environmental constraints individually, and beds with relatively lower HC were the most distinct in terms of community composition and structure. Species replacement was the main component of temporal variability and HC promoted community stability. While overall facilitative, the effects of HC might be taxa and trait‐dependent, justifying comprehensive trait‐based approaches. Our results reiterate the need to protect complex biogenic habitats.