Palaeoecological proxy data (pollen, non-pollen palynomorph (NPP), micro-charcoal, macro-charcoal, loss-on-ignition (LOI) and x-ray fluorescence (XRF)) recovered from lake sediments, cliff exposures, surface soils and moss pollsters within the eastern Andean cloud forest of Ecuador. Palaeoecological proxy data were recovered from lake sediments, surface soil and moss pollsters within the eastern Andean cloud forest of Ecuador. Materials and proxy data were collected with the aim of understanding how ecosystem dynamics were driven by anthropogenic, physical and climatic impact through time (late Quaternary). Here, data are provided for pollen, non-pollen palynomorph (NPP), micro-charcoal, macro-charcoal, loss-on-ignition (LOI) and x-ray fluorescence (XRF). Field samples were collected throughout 2012-2013 from the Napo province of Ecuador and analysed in the laboratory throughout 2014-2015 at The Open University (UK). Full details about this dataset can be found at https://doi.org/10.5285/952e8ddb-b573-44ad-a930-2c8c5164a381