This paper presents the environmental, climate and vegetation changes reconstructed for the last 14.6 kyr cal BP from the Marboré Lake sedimentary sequence, the highest altitude record (2612 m a.s.l.) in the Pyrenees studied up to date. We investigate the sensitivity of this high altitude site to vegetational and climate dynamics and altitudinal shifts during the Holocene by comparing palynological spectra of the fossil sequence and pollen rain content from current moss pollsters. We hypothesize that the input of sediments in lakes at such altitude is strongly controlled by ice phenology (ice-free summer months) and that during cold periods Pollen Accumulation Rate (PAR) and Pollen Concentration (PC) reflect changes in ice-cover and thus is linked to temperature changes. Low sedimentation rates and low PC and PAR occurred during colder periods as the Younger Dryas (GS-1) and the Holocene onset (12.6–10.2 kyr cal BP), suggesting that the lake-surface remained ice-covered for most of the year during these periods. Warmer conditions are not evident until 10.2 kyr cal BP, when an abrupt increase in sedimentation rate, PC and PAR occur, pointing to a delayed onset of the Holocene temperature increase at high altitude. Well-developed pinewoods and deciduous forest dominated the mid montane belt since 9.3 kyr cal BP until mid-Holocene (5.2 kyr cal BP). A downwards shift in the deciduous forest occurred after 5.2 kyr cal BP, in agreement with the aridity trend observed at a regional and Mediterranean context. The increase of herbaceous taxa during the late-Holocene (3.5 kyr cal BP-present) reflects a general trend to reduced montane forest, as anthropogenic disturbances were not evident until 1.3 kyr cal BP when Olea proportions from lowland areas and other anthropogenic indicators clearly expand. Our study demonstrates the need to perform local experimental approaches to check the effect of ice phenology on high altitude lakes sensitivity to vegetation changes to obtain more realistic reconstructions of mountain vegetation belts dynamics.