Key message Whole-crown ¹³C-pulse labelling can target tree canopy C fluxes in regions with dense understorey cover and investigate how increased photosynthetic C inputs may affect whole-ecosystem C fluxes. Abstract Climate change-driven increases in plant productivity have been observed at high northern latitudes. These trends are driven, in part, by the increasing abundance of tall shrub and tree species in arctic ecosystems, and the advance of treelines. Higher plant productivity may alter carbon (C) allocation and, hence, ecosystem C cycling and soil C sequestration. It is important to understand the contributions that the newly established canopy forming overstorey species makes to C cycling in these ecosystems. However, the presence of a dense understorey cover makes this challenging, with established partitioning approaches causing disturbance and potentially introducing measurement artefacts. Here, we develop an in situ whole-crown ¹³C-pulse labelling technique to isolate canopy C fluxes in areas of dense understorey cover. The crowns of five mountain birch (Betula pubescens ssp. czerepanovii) trees were provided with a ¹³CO₂ pulse using portable field equipment, and leaf samples were collected from neighbouring con-specific trees and hetero-specific understorey shrubs on days 1–10 and 377 post-crown labelling. We found effective and long-term enrichment of foliage in labelled trees, but no evidence of the ¹³C-signal in con- or hetero-specific neighbouring trees or woody shrubs. This method is promising and provides a valuable tool to isolate the role of canopy tree species in ecosystems with dense understorey cover.