The aim of this study was to draw a general picture of the phytoplankton community in peri-Alpine lakes, including for the first time a broad data set of six deep peri-Alpine lakes, belonging to the same geographical region. The objective was to define the main key drivers that influence the phytoplankton community composition in this particular vulnerable region, for which the impacts of climate change have been demonstrated to be stronger than on a global average. The phytoplankton was investigated with a particular focus on cyanobacteria and using a classification approach based on morpho-functional groups. We hypothesized that phytoplankton in peri-Alpine lakes is mainly driven by nutrient loads as well as by water temperatures, variables that are strongly influenced by climate change and eutrophication. Though different phytoplankton configurations among lakes were partly due to their geographical (altitude) position, assemblages were mostly linked to temperature and nutrients. Furthermore, the results confirmed the significant role of the spring fertilization on the seasonal phytoplankton development. Cyanobacteria were related to the increasing annual average of air and water temperature gradient and therefore might become more important under future warming scenario. Air temperatures have a significant impact on water temperature in the uppermost meters of the water column, with a stronger influence on warmer lakes.