Animals abandoned their ancestral marine niche and ventured into land multiple times across evolution, repeatedly overcoming major ecological challenges. These replicated evolutionary transitions constitute magnificent demonstrations of life’s capacity to evolve, and provide a rare opportunity to study the mechanisms driving large scale macroevolutionary convergence. However, the genomic underpinnings of the terrestrialization process remain largely unknown. Here, we investigated the macroevolutionary dynamics of gene repertoire evolution during convergent transitions out of the sea in molluscs. We find that despite deep temporal divergences, parallel expansions of ancient gene families played a major role in facilitating adaptation to non-marine habitats, highlighting the evolutionary potential of the pre-existing genomic toolkit. We further find evidence of functionally convergent lineage-exclusive gene gains, while overall family contractions seem mostly driven by neutral processes. Also, genomic innovations appear to have further fueled evolutionary independent habitat transitions. Collectively, these findings show that different evolutionary paths to genomic change (i.e. parallelism, convergence and innovation) can be simultaneously at play during major evolutionary transitions. Our results provide a genome-wide gene repertoire atlas of the molluscan terrestrialization that pave the way towards further understanding the functional and evolutionary bases of this process.