During the last century, temperate lakes have been strongly impacted by human eutrophication and climate change, causing shifts in phytoplankton communities and higher abundance of cyanobacteria. Paleolimnological reconstructions can extend the timeframe of observations beyond the extent of monitoring data and reveal long-term changes in aquatic communities. Existing paleolimnological studies often rely on proxies that are solely indicative of individual algal groups. As a result, reconstructing the overall algal community composition remains challenging. Here, we analyzed and cross-validated multiple proxies for phytoplankton community composition in sediment cores from three lakes on the Swiss Plateau that underwent extreme eutrophication in the 20^th century. We measured the relative abundance of phytosterols and phytol (phytol:sterol index, PSI) and hydrogen isotope offsets between C16:0 fatty acid and phytol (δ²H_{C16:0 Acid/Phytol}) and used these to detect past changes in the relative proportions of eukaryotic algae and cyanobacteria. We compared these new organic geochemical proxies with observational data and with gene amplicon sequence variants (ASVs) from plastid-derived 23S rRNA. PSI and δ²H_{C16:0 Acid/Phytol}values were generally in good agreement with cyanobacterial 23S rRNA ASVs, and all proxies indicated increasing proportions of cyanobacteria in response to eutrophication. However, our study also revealed potential biases associated with each individual algal proxy. Specifically, δ²H_{C16:0 Acid/Phytol}values were impacted by non-algal lipid sources, while the abundance of small coccoid cyanobacterial taxa was overestimated by 23S rRNA ASVs relative to their biovolume. Still, the combination of PSI and δ²H_{C16:0 Acid/Phytol}values with other algal proxies is a promising tool for tracing the long-term relative abundance of cyanobacteria and could provide a comprehensive picture of changes in phytoplankton communities over millennial timescales.