Arctic marine ecosystems are becoming more boreal due to climate change. Predictions of ecosystem change focus mainly on Arctic inflow or interior shelves, with few comprehensive studies on Arctic outflow regions. During September–October 2017, soft-bottom communities were sampled and benthic ecosystem processes were quantified at 12 stations on the Northeast Greenland shelf (outflow shelf) and compared to the last regional ecosystem study, conducted in 1992 and 1993. The benthic habitat was characterized in terms of sediment granulometry, pigment concentrations, and porewater chemistry (dissolved inorganic carbon, nutrients). Total abundance and biomass of macrobenthos and meiobenthos, bacterial abundance, porewater dissolved inorganic carbon and ammonium concentrations were higher on the outer shelf compared to locations adjacent to the Nioghalvfjerdsfjorden glacier at 79°N and the inner shelf stations (e.g., macrofauna: 1,964–2,952 vs. 18–1,381 individuals m⁻²). These results suggest higher benthic production in the outer parts of the NEG shelf. This difference was also pronounced in macrobenthic and meiobenthic community structure, which was driven mainly by food availability (pigments with 1.3–4.3 vs. 0.3–0.9 µg g⁻¹ sediment, higher total organic carbon content and bacterial abundance). Compared to the early 1990s, warmer bottom water temperatures, increased number of sea-ice-free days and lower sediment pigment concentrations in 2017 were accompanied by decreased polychaete and increased nematode abundance and diversity, and a different community structure of nematode genera. The present study confirms previous reports of strong pelagic-benthic coupling on the NEG shelf, but highlights a possible weakening since the early 1990s, with a potential shift in importance from macrofauna to meiofauna in the benthic community. Increasing inflow of Atlantic water and decreasing volume transport and thickness of sea ice through the Fram Strait, probably affecting the Northeast Water Polynya, may be responsible, suggesting ecosystem-wide consequences of continued changes in sea-ice patterns on Arctic shelves.