Thermal damage, high osmolarity, and ethanol toxicity in the yeast Saccharomyces cerevisiae limit titer and productivity in fermentation to produce ethanol. We show that long-term adaptive laboratory evolution at 39.5°C generates thermotolerant yeast strains, which increased ethanol yield and productivity by 10% and 70%, in 2% glucose fermentations. From these strains, which also tolerate elevated-osmolarity, we selected a stable one, namely a strain lacking chromosomal duplications. This strain (TTY23) showed reduced mitochondrial metabolism and high proton efflux, and therefore lower ethanol tolerance. This maladaptation was bolstered by reestablishing proton homeostasis through increasing fermentation pH from 5 to 6 and/or adding potassium to the media. This change allowed the TTY23 strain to produce 1.3-1.6 times more ethanol than the parental strain in fermentations at 40°C with glucose concentrations~300 g/L. Furthermore, ethanol titers and productivities up to 93.1 and 3.87 g·L −1 ·hr −1 were obtained from fermentations with 200 g/L glucose in potassium-containing media at 40°C. Albeit the complexity of cellular responses to heat, ethanol, and high osmolarity, in this study we overcome such limitations by an inverse metabolic engineering approach.ethanol tolerance, high-temperature fermentation, S. cerevisiae, thermotolerance Abbreviations: AcetylCoA, acetyl coenzyme-A; ADH, alcohol dehydrogenase; ADH4, alcohol dehydrogenase (alcohol dehydrogenase isoenzyme type IV); ADP, adenosine-diphosphate; ALD2, aldehyde dehydrogenase (cytoplasmic aldehyde dehydrogenase); ATP, adenosine-triphosphate; ATP_F0, ATP synthase, F1 complex (membrane-embedded portion; protons are transferred through this); ATP_F1, ATP synthase, F1 complex (hydrophilic catalytic portion which is sticking into matrix); ATP-Stalk, ATP synthase stalk (it is considered as part of F1); bc1, cytochrome B (mitochondrial cytochrome bc1 complex); CytC, cytochrome C oxidase; Glucose-P, glucose-6-phosphate; Glyceraldehyde-P, glyceraldehyde-3-phosphate; GND1, 6-phosphogluconate dehydrogenase; HSP30, heat shock protein 30 (negative regulator of the H + -ATPase PMA1); IDP1, isocitrate dehydrogenase, NADP-specific (mitochondrial NADP-specific isocitrate dehydrogenase); KHA1, K/H ion antiporter (putative K + /H + antiporter); MDH1, malate dehydrogenase (mitochondrial malate dehydrogenase); MPC1, mitochondrial pyruvate carrier (mitochondrial inner membrane complex that mediates pyruvate uptake); MPC3, mitochondrial pyruvate carrier (highly conserved subunit of the mitochondrial pyruvate carrier); NADPH, nicotinamide adenine dinucleotide reduced; NDE1, NADH dehydrogenase, external (mitochondrial external NADH dehydrogenase; type II NAD(P)H:quinone oxidoreductase that catalyzes the oxidation of cytosolic NADH); NDE2, NADH dehydrogenase external (mitochondrial external NADH dehydrogenase; catalyzes the oxidation of cytosolic NADH); NDI1, NADH dehydrogenase internal (NADH: ubiquinone oxidoreductase; transfers electrons from NADH to ubiquinone in respiratory chain ...