Allelochemical interactions are likely to be a contributing factor explaining the success of large blooms of the harmful marine dinoflagellate Alexandrium, however, the physiological mechanisms of allelochemical interactions remain poorly described. Here we investigated the sub-lethal effects (on an hourly scale) of a filtrate containing allelochemicals from Alexandrium minutum on the physiology of the common diatom Chaetoceros muelleri. The filtrate induced deleterious effects to the diatom physiology within only 30 min of exposure. Esterase activity and photosynthesis were drastically inhibited, with up to 34% of the population being metabolically inactive and up to 30% reduction in photosystem II quantum yield when exposed to the filtrate. In addition, intracellular reactive oxygen species increased by 26% in response to allelochemical exposure. C. muelleri pigment and lipid analyses indicated that the photosystem II was inhibited, with photoinhibition-like responses (activation of xanthophyll cycles, and changes in associated lipids) upregulated to mitigate the toxic effects of allelochemicals. Changes in the proportions of membrane lipid classes and increased membrane fatty acids saturation by 9% may be an attempt to maintain membrane integrity and associated enzyme activity, or could be the result of deleterious effects on membranes. An 8% decrease in cellular storage lipids (triglycerides) revealed a mobilization of energy suggesting an energetic cost for the diatom to counteract the allelochemical effects. We hypothesize that the rapid alteration of physiological functions such as photosynthesis and some enzymatic activities may result from direct damage on external membranes. Overall this study describes the sub-lethal mechanisms and provides useful biomarkers to understand the role of allelochemical interactions and associated ecological processes in structuring plankton communities.