This paper examines how perennial Aster tripolium and annual Salicornia procumbens salt marshes alter the biomass, density, taxon diversity, and community structure of benthic macrofauna, and also examines the role of elevation, sediment grain size, plant cover, and marsh age. Core samples were collected on a fixed grid on an intertidal flat in the Westerschelde estuary (51.4° N, 4.1° E) over 5 years (2004–2008) of salt marsh development. In unvegetated areas, macrobenthic biomass, density, and taxon diversity were highest when elevation was highest, benthic diatoms were most abundant, and sediment median grain size was smallest. In contrast, in salt marsh areas, macrobenthic biomass and taxon diversity increased with median grain size, while the effects of elevation and diatom abundance on macrobenthic biomass, density, and diversity were not significant. In fine sediments, macrofaunal community structure in the salt marsh was particularly affected; common polychaetes such as Nereis diversicolor, Heteromastus filiformis, and Pygospio elegans had low abundance and oligochaetes had high abundance. Marsh age had a negative influence on the density of macrofauna, and A. tripolium stands had lower macrofaunal densities than the younger S. procumbens stands. There were no significant effects of marsh age, plant cover, and vegetation type on macrobenthic biomass, taxon diversity, and community structure. The results highlight that ecosystem engineering effects of salt marsh plants on macrofauna are conditional. Organic enrichment of the sediment and mechanical hindering of macrofaunal activity by plant roots are proposed as plausible mechanisms for the influence of the salt marsh plants on macrofauna.