Phytoplankton time-series enable the observation of recurrent seasonal patterns on community composition, but drastic shifts in community structure are rarely observed, unless linked to anthropogenic impacts (e.g. changes in nutrient inputs). Here, we report a unique case of non-seasonal, multiannual regime shift of phytoplankton community structure in Lake Kivu, East Africa, and explore the possible causes for such changes. We recorded phytoplankton biomass every 2 weeks over a period of 12 years (from 2002 to 2015). Phytoplankton community previously dominated by cyanobacteria and diatoms changed considerably from 2012, with a conspicuous rise in the biomass of green algae (from 3 to 33% lake-wide), and a decline of cryptophytes and cyanobacteria along with an increase in total chlorophyll a concentration. Concomitantly, we observed significant differences in the mixed layer depth between the two periods, resulting from changes in the thermal gradient. The euphotic zone depth was also reduced in 2012–2015, probably from the higher phytoplankton biomass. Moreover, mean particulate nitrogen and phosphorus increased as well as the particulate N:P ratio. Desmids (Cosmarium laeve) now dominate the mixolimnion, probably due to atelomixis, observed in high-frequency temperature measurements. We believe that decadal or multidecadal variability of climate on the Indian Ocean may be the reason for this regime shift in thermal stratification, with a strong impact in phytoplankton community structure. In conclusion, our study demonstrates that tropical lakes may be subject to non-seasonal fluctuations that generate multiannual regime shifts. These regime shifts have probably never been reported previously because of the lack of long phytoplankton time-series in low latitudes.