Coastal soft sediment habitats contain highly productive benthic communities that provide numerous ecological services. Many of these functions, processes and services are underpinned by the behaviour, density and diversity of the resident macrofaunal community. Climate change has caused heat waves to become more regular and extreme, causing die-off’s of functionally important shellfish beds, potentially generating large shifts in benthic community structure and functioning. Recent studies of the New Zealand intertidal cockle (Austrovenus stutchburyi) dieoff events have focused on cockle population recovery, but there is very little understanding of how the rest of the macrofaunal community responds. To understand how the macrofaunal communities respond to cockle-die offs, a manipulative experiment was undertaken at 23 sites in four estuaries on the northeast coast of the North Island. In late summer, at each site we established a 9m2 control and 9m2 exclusion plot. One year later, we sampled all plots for macrofauna and sediment properties. Results indicate a strong relationship between treatment type and community composition, with none of the exclusion treatments returning to predisturbance community compositions. Furthermore, that recovery was largely estuary specific and community composition following disturbance was highly variable within exclusion treatments. Statistical analysis highlighted that exposure to high intensity wind-wave activity and polychaete dominance within estuaries could explain the relatively improved recovery of Ongare sites within Tauranga harbour. Additionally, there are observable variations in cockle recruitment between sites for both adults and juveniles. This experiment explores whether the removal of cockles, as key habitat forming species, selects for a different macrofaunal community type. The observed changes in community structure can be linked to shifts in ecosystem functioning in these soft sediment habitats.