Lake Kivu, East Africa, is a deep oligotrophic and meromictic lake containing high amounts of dissolved methane (∼55–60 km3) and carbon dioxide (∼300 km3) in its deep waters. Methane harvesting for energy production began in 2015, and a monitoring programme was set up to assess possible disturbance on the ecosystem. Phytoplankton biomass and composition was assessed twice per month or monthly at 2 monitoring sites between June 2005 and December 2019, based on HPLC analysis of chlorophyll a (Chl-a) and marker pigments. This long-term series shows that significant changes occurred around 2010 in the lake phytoplankton, with a notable increase of Chl-a and changes in the assemblage toward an increase in non-motile green algae and diatoms. To assess possible changes due to methane harvesting, we compared 2 periods, 2012–2014 and 2018–2019. Chl-a concentration decreased slightly in 2018–2019 compared to the reference period of 2012–2014, and significant changes occurred in composition of the phytoplankton assemblage. In terms of relative contribution to Chl-a, diatoms increased from 26% to 46%, whereas green algae decreased ∼2-fold, from 35% in 2012–2014 to 18% in 2018–2019. Multivariate analyses showed that phytoplankton composition was influenced by seasonal and interannual variations of limnological variables related to changes in meteorological factors. To assess possible future changes due to methane exploitation, we recommend increasing sampling frequency and taxonomic resolution, as well as improving environmental data acquisition.