Conventional sedimentological models of alluvial fan sequences tend to be based on fans in subsiding sedimentary basins. Fans in uplifting terrains are rather different. We examined the sequence of fan delta and alluvial fan deposition from the Pliocene to the Late Quaternary in the uplifting terrain of the Neogene sedimentary basins of Almería, Betic Cordillera, SE Spain. There were three phases of fan deposition, each yielding particular morpho-sedimentological characteristics and each having distinctive spatial distributions. The first phase was the Pliocene fan deltas, deposited where the larger river systems entered the receding early Pliocene seas. This phase was followed during the late Pliocene–Early Pleistocene by a phase of extensive alluvial fan deposition extending from the mountain fronts to the basin centres. Continued uplift occurred during the Pleistocene, resulting in incision of the drainage network and dissection of the Plio-Pleistocene fan systems. The third phase, during the Quaternary, involved much smaller mountain front alluvial fans set well below the Plio-Pleistocene fans, except in local areas of tectonic subsidence where extensive fans were formed. The older fans exhibit stacked sedimentary successions with very little evidence of sustained vertical incision. However, the Quaternary fans show much evidence of sustained incision between major aggradational phases, often resulting in inset rather than stacked stratigraphic relationships. We interpret this to imply that, although the tectonic context was the primary temporal control on variations within the older fan successions, within the Quaternary fans the overall tectonic control has been modified by responses to the Quaternary climatic sequence.