In semi-arid regions such as the Mediterranean, which are subject to rising temperatures and increased drought as a result of future global climate change, we need to develop our understanding of environmental responses to past climatic shifts. Mountainous regions are considered one of the most fragile environments across the globe, and are suffering from increased pressures from both climatic changes and anthropogenic activity. The biological and bioclimatic diversity of the Middle Atlas Mountains provides a crucial case study for semi-arid ecosystems, and the use of palaeoecology in this region will provide key insights into past vegetation dynamics under a range of boundary conditions. Pioneering work in understanding Holocene environmental change in the Middle Atlas was conducted over 20 years ago, and the pace of work in the region is now accelerating. However, to date, few high-resolution, full-Holocene records from this region exist. After conducting an investigation into the comparability of vegetation records produced using the traditional method of pollen preparation (with hydrofluoric acid) and those produced using the dense-media separation method, this study presents three records from the Middle Atlas Mountains: two full-Holocene records from a lacustrine environment and a semi-terrestrial bog, and a late Holocene record from a second semi-terrestrial bog. This study provides valuable insights into the long-term climatic trend over the Holocene, and the shift from dry, oceanic conditions with high seasonality in the early Holocene, towards more moist, continental conditions with lower seasonality in the late Holocene. The nature of the spread of Cedrus across the Middle Atlas during the Holocene is discussed in detail, indicating that altitude and geographical location were key controlling factors. This study also provides the first evidence of the 8.2 ka event in Morocco, as well as warming and cooling associated with the Medieval Climate Anomaly and the Little Ice Age, respectively, in the late Holocene. The first high-resolution, contiguous microcharcoal record from the Middle Atlas is presented here, highlighting Holocene fire regime changes and correlating key fire episodes with North Atlantic Bond Events. Finally, the study provides detailed insights into the nature and timing of anthropogenic activity in the region, with two clear phases of activity: low-level activity from c. 4500 years ago onwards, and much more intense activity over the last 1000 years.