The upper parts of the floor cumulates of the Skaergaard Intrusion, East Greenland, contain abundant features known as troughs. The troughs are gently plunging synformal structures comprising stacks of crescentic modally graded layers with a sharply defined mafic base that grades upward into plagioclase-rich material. The origin of the troughs and layering is contentious, attributed variously to deposition of mineral grains by magmatic currents descending from the nearby walls, or to in situ development by localised recrystallisation during gravitationally-driven compaction. They are characterised by outcrop-scale features such as mineral lineations parallel to the trough axis, evidence of erosion and layer truncation associated with migration of the trough axis, and disruption of layering by syn-magmatic slumping. A detailed microstructural study of the modal trough layers, using electron backscatter diffraction together with geochemical mapping, demonstrates that these rocks do not record evidence for deformation by either dislocation creep or dissolution–reprecipitation. Instead, the troughs are characterised by the alignment of euhedral plagioclase crystals with unmodified primary igneous compositional zoning. We argue that the lineations and foliations are, therefore, a consequence of grain alignment during magmatic flow. Post-accumulation amplification of the modal layering occurred as a result of differential migration of an unmixed immiscible interstitial liquid, with upwards migration of the Si-rich conjugate into the plagioclase-rich upper part of the layers, whereas the Fe-rich immiscible conjugate remained in the mafic base. Both field and microstructure evidence support the origin of the troughs as the sites of repeated deposition from crystal-rich currents descending from the nearby chamber walls. Electronic supplementary material The online version of this article (10.1007/s00410-018-1466-1) contains supplementary material, which is available to authorized users.