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Quantitative climate reconstructions from pollen typically rely on empirical relationships between pollen abundances or assemblages and climate, such as the modern analogue technique. However, these techniques may be problematic when applied to fossil sequences, as they cannot separate anthropogenic from climatic influence on pollen assemblages. Here, we reconstruct Mid- to Late Holocene summer aridity in the Middle Atlas, Morocco, using stable carbon isotope analysis of isolated fossil Cedrus pollen. This approach is based on well-documented plant physiological responses to moisture stress and is therefore independent of vegetation composition. We find that there has been a general long-term trend of increasing summer aridity in the region during the last 5000 years to the present day. The gradual decline of Cedrus atlantica forest in the Late Holocene follows this aridity trend. Additionally, we show how isolating a specific pollen type for carbon isotope analysis yields a robust climate signal, versus using pollen concentrates or bulk sediment. Our findings indicate that climate has become drier in the region and confirms the Mid- to Late Holocene aridification trend observed more widely in the western Mediterranean, using a novel proxy for this region with good potential for wider application in other environments.