The impact of climate change on forest ecosystems is context-dependent. Simulation studies in European mountain forests showed critical transitions in composition and structure, even in the presence of topographical refugia. However, little is known about climate change impacts on Atlantic lowland forests, where topographic complexity is largely lacking. To address this knowledge gap, we used the “iLand” model to examine potential shifts in forest composition and structure under various climate and disturbance regimes in a beech-dominated Atlantic lowland forest landscape in Flanders (Belgium) over 1000 years. Results show that composition and structure may rapidly shift if temperature rises over + 2 °C and summer precipitation drops by more than 40%. Under such a “hot dry” projection, black pine (Pinus nigra [Arnold]) will become the dominant species, and timber volume decreases by up to 34%. Lowland beech forests are expected to withstand temperature increases, beyond 2 °C increase, provided that summer precipitation remains at current levels. Natural disturbances impacts by wind and bark beetles could increase by up to 193% under the hot dry climate projections. Additionally, we discovered that fine-textured soils may serve as a refugium for drought-sensitive species in lowland forests, taking a similar role as topographical refugia in mountain forests. Our study suggests threshold behaviour of lowland forests under warmer and drier conditions, which could threaten levels of ecosystem service provisioning for the future. Thus, it is imperative to limit climate change to moderate levels, and to consider the role of soils in future lowland forest ecosystem dynamics.