As part of the HAUSGARTEN long-term observatory, sediment trap deployments were carried out before, during, and after the anomalously warm Atlantic Water inflow observed from 2005 to 2007 in the eastern Fram Strait. Downward export of particulate organic carbon (POC), zooplankton fecal pellet carbon (FPC), and biogenic particulate silica (bPSi) were measured from August 2002 to June 2003 and from July 2004 to July 2008 to indirectly assess the impact of the warm anomaly on phytoplankton and zooplankton communities in the region. Lower and less frequent bPSi fluxes were observed during most of the warm anomaly period, reflecting a shift in phytoplankton community composition towards dominance of small-sized phytoplankton under warmer conditions. Lower FPC fluxes observed concurrently with the lower bPSi fluxes may indicate a decrease in fecal pellet production due to changing feeding conditions. In addition, the export of smaller fecal pellets in fall 2005 and spring 2006 suggests a dominance of smaller zooplankton during the warm anomaly. Nonetheless, bPSi and FPC export always increased in the presence of ice cover in the area above the sediment trap, even during the warm anomaly period, suggesting that sea ice is a key factor influencing the frequency of export events in the eastern Fram Strait. The scarcity of ice over the sampling area in 2005 and 2006 may partly be due to the warm anomaly, although solar radiation and ice drift due to wind stress also govern ice cover extent in the region. Overall, the warm anomaly resulted in a shift in the composition of the export fluxes when associated with an absence of ice cover in the eastern Fram Strait.