Microphytobenthos (MPB) are an important nitrogen (N) sink in coastal systems, but little is known about the fate of this N after it has been assimilated. We used an in situ 15N pulse‐chase experiment in subtidal sands to follow the assimilation, trophic transfer, transformation, and flux pathways of MPB‐N over 33 d. Throughout the study MPB dominated 15N uptake, on average representing only 18.1% of the biomass but 63.9% of the 15N within 0–2 cm sediment. Following assimilation, 15N was rapidly transferred to deeper sediment, with 32.1% below 2 cm and 16.5% below 5 cm after 60 h. In contrast to MPB, bacteria represented 39.5% of sediment biomass but accounted for only up to 27.3% of assimilated 15N. Foraminifera accumulated and stored 15N more than bacteria; their contribution to the 15N remaining in 0–2 cm sediment at the end of the study was more than double their biomass contribution. Thirty‐three days after the 15N was assimilated by MPB 27% remained in the sediment, 16.5% had been effluxed as
NO3−, 20.8% had been effluxed as
NH4+, 20.7% had been effluxed as N2 and 15.1% was missing. Most (12.6%) of 15N label that was missing at the end of the study was probably lost as dissolved organic N (DON) fluxes. Of the 15N remaining in 0–2 cm sediment, 80.4% was in MPB, 2.7% in bacteria, 1% in foraminifera and the remaining 15.9% was uncharacterized. Overall there was little benthic trophic transfer with most of the MPB‐assimilated N remineralized over 33 d.