Intense disturbance may locally destroy patches of habitat and shape the landscape into a mosaic of reassembling communities. The development of ecosystem properties during such community reassembly is poorly understood. In intertidal bare sediments, trophic relations between microphytobenthos or heterotrophic bacteria and macrofauna invertebrates may guarantee fundamental ecosystem properties such as carbon flow through the food web. We studied the dynamic relation between reassembling macrofauna communities and such microbial carbon flow during recovery after severe disturbance. We deliberately induced prolonged hypoxia in winter and early summer and allowed recolonisation for periods of two and five months. Carbon flow was quantified from basal resources (microphytobenthos and bacteria) to intermediate consumers using 13C as a tracer. Within the period of study (5 months), microbial carbon flow fully recovered, although macrofauna diversity was still very low compared to the natural communities (ranging from 6 to 17 species). More than 90% of microbial carbon flow to macrofauna was due to the consumers that recolonised within two months. Two of these species were dominant contributors to microphytobenthos carbon transfer to fauna. Furthermore, at an early stage of reassembly, this ecosystem property was remarkably similar when disturbance took place at different times of the year (winter or early summer), although there were differences in assemblage composition and functional diversity. We conclude that species assemblages and ecosystem function developed relatively independently in this benthic system. We discuss which ecological factors may have caused such non-parallel development of macrofaunal communities and carbon flow.