Decades of eutrophication in Danish estuaries have changed the dominant primary producers from eelgrass (Zostera marina) meadows to phytoplankton and ephemeral macroalgae. This has resulted in enrichment of sediments with organic matter, and frequent bottom-water hypoxia that negatively affects the macrofauna community. In this study, we propose that restoration by sand-capping is a solution to improve sediment conditions, which may facilitate eelgrass restoration and accelerate recovery of macrofauna communities. Sand-capping was carried out by adding a layer of approximately 10 cm of sand on top of 1.4 ha of organic-rich sediment. One year later, we transplanted 6000 eelgrass shoots onto the sand-cap; however, they did not survive more than a few months due to blooms of filamentous algae that smothered the eelgrass. The sand-cap remained intact and the colonization of macrofauna was investigated by analysis of species richness (S), abundance (N) and feeding guilds (FGs) in the sand-capped area and at uncapped sediment. S, N and diversity of FGs were significantly higher for infauna in the sand-capped area compared to uncapped sediment after 1 yr. Conversely, S of epifauna was highest on uncapped sediment and N of epifauna varied seasonally rather than being affected by the sediment conditions.