Diatoms are photosynthetic microorganisms of great ecological and biogeochemical importance, forming vast blooms in diverse aquatic ecosystems. They are subjected to a wide range of environmental cues, including abiotic stressors and biotic interactions with associated bacteria, viruses and grazers. However, the cellular strategies that underline their ecological success and their rapid acclimation to fluctuating conditions are still underexplored. This study investigates heterogeneity within diatom populations in response to oxidative stress, which mediates a wide range of environmental stress conditions. We combined flow cytometry and a microfluidics system for live-imaging microscopy to measure redox dynamics at the single-cell level. Using the redox-sensitive sensor roGFP we measured in vivo organelle-specific oxidation patterns in the model diatom Phaeodactylum tricornutum. Chloroplast targeted roGFP exhibited a light-dependent, bi-stable oxidation pattern in response to oxidative stress, revealing two distinct subpopulations. Remarkably, the “oxidized” subpopulation was sensitive to the stress and subsequently died, while the “reduced” subpopulation was resilient to it and recovered. We further characterized an early phase of “pre-commitment” to cell death following oxidative stress, after which cell death was irreversibly activated in the “oxidized” cells, even upon removal of the stress. Oxidation of the chloroplast glutathione pool preceded commitment to cell death, and was used as a novel predictor of cell fate. We propose that phenotypic variability within diatom populations can provide an ecological strategy to cope with rapid environmental fluctuations in the marine ecosystem.