John Allen made many contributions to quantitative sedimentology, particularly in experimental sedimentation (dynamical significance of current structures), alluvial sedimentation (low- and high-sinuosity streams) and deltaic sedimentation (large deltas formed under conditions of high energy).

His outstanding work was notable for the way in which it is brought to bear on problems concerning the origin, transport, depositional environments and tectonic significance of the Old Red Sandstone. His three textbooks are widely used in the earth sciences and his many critical reviews have stimulated other workers. Overall, his integrated approach profoundly influenced sedimentary research and thereby a broad area of geology.

After his retirement, John collaborated and published extensively with archaeologists in Britain on the identification and use of geological materials in past societies and the exploitation of the Severn Estuary by humans.