The impact of the ca. 75 ka Mount Toba (Indonesia) supereruption on regional and global climate has been controversial. East Africa is pivotal for qualifying this impact, specifically in addressing a hypothesis that this eruption caused a volcanic winter leading to a genetic bottleneck in anatomically modern human populations. If the Toba eruption caused a volcanic winter in East Africa, effects should be recorded in sediments from climatologically sensitive ecosystems. In deep tropical lakes, cooler temperatures would have reduced the density contrast between the epilimnion and hypolimnion, causing increased mixing, hypolimnion oxygenation, and enhanced nutrient advection. Such environmental changes produce noticeable and predictable responses in lake fossil assemblages and sediment loading. Here we present the first paleoecological evidence from East Africa of environmental conditions surrounding the eruption in a high-resolution (∼8–9 yr) analysis of two cores collected by the Lake Malawi Drilling Project. These cores contain an undisturbed record of sedimentation before, during, and after deposition of the youngest Toba Tuff. Concentrations of climate-sensitive ecological indicators such as phantom midges, diatoms, and other algae through a >270 yr interval bracketing the Toba cryptotephra show no unusual or sustained deviations from background variability within Lake Malawi associated with the hypothesized post-Toba cooling. We find no evidence for significantly enhanced mixing or ecosystem disturbance that would be anticipated following a volcanic winter.