Fram Strait, the deep gateway to the Arctic Ocean, appears to be highly affected by the consequences of global warming, which is leading to changes in the physical environment through rising water temperatures and loss of sea ice cover. Understanding the dynamics of plankton communities in this scenario is critical for assessing ecosystem services. Therefore, we here present data from two decades of plankton summer season observations of the upper water column at the Long-Term Ecological Research observatory HAUSGARTEN and the Helmholtz Infrastructure Program FRAM in the eastern Fram Strait. We started with microscopy and chlorophyll-a measurements of water column samples and continuously added more parameters of the entire microbial cycle, including in-depth biodiversity studies. Since 2011 also the mesozooplankton population dynamics have been monitored. In situ observations are complemented by satellite data on major phytoplankton groups to understand variability and trends in the whole area also at times when in situ sampling was not possible. Our results showed an increase in chlorophyll-a from 2007 to 2012, after a warm anomaly in the eastern Fram Strait (2005-2008) followed by a slight decrease. Diatoms were dominant prior to the anomaly, while flagellate-dominated communities occurred with changing contributions from Phaeocystis spp. thereafter. Inter-annual and seasonal variability appears to be considerable, emphasizing the need for further regular observations to confirm whether we are observing true long-term trends or inter/intra-annual variation.