Aim: Coastal infrastructures are increasing at different latitudes, and their deployment often results in a complete replacement of natural habitats. Although infrastructure provides novel habitats, ecological engineering can increase their similarity to natural rocky habitats. One hurdle for effective design of greener infrastructure is the scarce information on the processes that underpin differences in the structure of communities between built and natural habitats. Using long-term data of intertidal community structure, we tested whether the magnitude of between-habitat differences changes with breakwater age and across latitudes, and we examined the role of topographic microhabitats (i.e., rock pools) in driving these differences. Location: Nine locations distributed from 18 to 41°S. Time period: 2016–2020. Methods: We sampled the mid-intertidal community structure on breakwaters of different age and on natural rocky habitats (platforms and boulder fields) and assessed the availability of microhabitats, such as crevices and rock pools, along a coastline spanning 23° of latitude. Using generalized additive models (GAMs), we assessed the effect of the different factors on species diversity and functional group abundances. Results: Age since construction was a poor predictor of differences between breakwaters and natural habitats. Communities on older breakwaters bore a poor resemblance to the species composition or functional group abundances found in natural habitats. The magnitude of differences between breakwaters and natural habitats varied with latitude, with season and with the type of natural habitat attributable to differences in microhabitats, especially in rock pool availability. Conclusions: Our results indicate that replacement of rocky habitats with breakwaters will cause permanent alterations to coastal ecosystems. Our findings suggest that the availability of microhabitats able to shelter species from stressful environmental conditions is more important at lower and intermediate latitudes; hence, they should be incorporated primarily into infrastructures in tropical or subtropical areas. These strategies could help to compensate for the impacts on rocky ecosystems associated with increases in coastal urbanization.