High mountain zones in the Mediterranean area are considered more vulnerable in comparison to lower altitudes zones. Lefka Ori massif, a global biodiversity hotspot on the island of Crete is part of the Global Observation Research Initiative in Alpine Environments (GLORIA) monitoring network. The paper examines species and vegetation changes with respect to climate and altitude over a seven-year period (2001–2008) at a range of spatial scales (10 m Summit Area Section-SAS, 5 m SAS, 1 m2) using the GLORIA protocol in a re-survey of four mountain summits (1664 m–2339 m). The absolute species loss between 2001–2008 was 4, among which were 2 endemics. At the scale of individual summits, the highest changes were recorded at the lower summits with absolute species loss 4 in both cases. Paired t-tests for the total species richness at 1 m2 between 2001–2008, showed no significant differences. No significant differences were found at the individual summit level neither at the 5 m SAS or the 10 m SAS. Time series analysis reveals that soil mean annual temperature is increasing at all summits. Linear regressions with the climatic variables show a positive effect on species richness at the 5 m and 10 m SAS as well as species changes at the 5 m SAS. In particular, June mean temperature has the highest predictive power for species changes at the 5 m SAS. Recorded changes in species richness point more towards fluctuations within a plant community’s normal range, although there seem to be more significant diversity changes in higher summits related to aspects. Our work provides additional evidence to assess the effects of climate change on plant diversity in Mediterranean mountains and particularly those of islands which remain understudied.