To evaluate how mangrove invasion and removal can modify short-term benthic carbon cycling and ecosystem functioning, we used stable-isotopically labeled algae as a deliberate tracer to quantify benthic respiration and C-flow over 48 h through macrofauna and bacteria in sediments collected from (1) an invasive mangrove forest, (2) deforested mangrove sites 2 and 6 years after removal of above-sediment mangrove biomass, and (3) two mangrove-free control sites in the Hawaiian coastal zone. Sediment oxygen consumption (SOC) rates averaged over each 48 h investigation were significantly greater in the mangrove and mangrove removal site experiments than in controls and were significantly correlated with total benthic (macrofauna and bacteria) biomass and sedimentary mangrove biomass (SMB). Bacteria dominated short-term C-processing of added microalgal-C and benthic biomass in sediments from the invasive mangrove forest habitat and in the 6-yr removal site. In contrast, macrofauna were the most important agents in the short-term processing of microalgal-C in sediments from the 2-yr mangrove removal site and control sites. However, mean faunal abundance and C-uptake rates in sediments from both removal sites were significantly higher than in control cores, which collectively suggest that community structure and short-term C-cycling dynamics of sediments in habitats where mangroves have been cleared can remain fundamentally different from un-invaded mudflat sediments for at least 6-yrs following above-sediment mangrove removal. In summary, invasion by mangroves can lead to dramatic shifts in benthic ecosystem function, with sediment metabolism, benthic community structure and short-term C-remineralization dynamics being affected for years following invader removal.