Corals and gorgonians play an important role as ecosystem engineers in many sublittoral communities worldwide. However, coral populations are being increasingly impacted by human activities. Active ecological restoration is a popular conservation tool nowadays, widely used to revert degradation in natural populations. Several studies have reported survival and growth success in actively restored corals, but few have studied the long‐term effect of transplantation on coral reproduction. We investigated survival and sexual reproduction of transplanted colonies of the Mediterranean gorgonian Eunicella singularis up to 3 years after being recovered from fishery bycatch and transplanted back to their habitat. Three different colony sizes were tested to explore possible effects of fragmentation on survival and reproduction. Results showed that transplanted colonies suffered a significant mortality during the first 4–5 months (30–35%), independently of fragment size. However, larger fragments showed high survival despite other disturbances, as a bloom of ephemerons filamentous algae occurred during the study. Results also showed that reproductive capacity is negatively affected by transplantation in female colonies. Conversely, male colonies were not directly affected by transplantation but showed an unexpectedly reduced number of spermary sacs both in transplanted and natural control colonies. The trade‐off between investment in reproduction and mortality of transplants highlights that large colony size could be the most appropriate for the active restoration of E. singularis. This study emphasizes the need to explore the long‐term viability and the reproduction investment in transplanted corals as indicators of restoration success, whose populations are sustained by sexual reproduction.