AbstractEthanol fermentations can be prematurely halted asSaccharomyces cerevisiaefaces adverse conditions, such as acidic pH, presence of acetic acid, and supraoptimal temperatures. The knowledge on yeast responses to these conditions is essential to endowing a tolerant phenotype to another strain by targeted genetic manipulation. In this study, physiological and whole-genome analyses were conducted to obtain insights on molecular responses which potentially render yeast tolerant towards thermoacidic conditions. To this end, we used thermotolerant TTY23, acid tolerant AT22, and thermo-acid tolerant TAT12 strains previously generated by adaptive laboratory evolution (ALE) experiments. The results showed an increase in thermoacidic profiles in the tolerant strains. The whole-genome sequence revealed the importance of genes related to: H+, iron, and glycerol transport (i.e.,PMA1,FRE1/2,JEN1,VMA2,VCX1,KHA1,AQY3, andATO2); transcriptional regulation of stress responses to drugs, reactive oxygen species and heat-shock (i.e.,HSF1,SKN7,BAS1,HFI1, andWAR1); and adjustments of fermentative growth and stress responses by glucose signaling pathways (i.e.,ACS1,GPA1/2,RAS2,IRA2, andREG1). At 30 °C and pH 5.5, more than a thousand differentially expressed genes (DEGs) were identified in each strain. The integration of results revealed that evolved strains adjust their intracellular pH by H+and acetic acid transport, modify their metabolism and stress responses via glucose signaling pathways, control of cellular ATP pools by regulating translation and de novo synthesis of nucleotides, and direct the synthesis, folding and rescue of proteins throughout the heat-shock stress response. Moreover, the motifs analysis in mutated transcription factors suggested a significant association of SFP1, YRR1, BAS1, HFI1, HSF1, and SKN7 TFs with DEGs found in thermoacidic tolerant yeast strains.Key points•All the evolved strains overexpressed the plasma membrane H+-ATPase PMA1 at optimal conditions•Tolerant strain TAT12 mutated genes encoding weak acid and heat response TFs HSF1, SKN7, and WAR1•TFs HSF1 and SKN7 likely controlled the transcription of metabolic genes associated to heat and acid toleranceSupplementary InformationThe online version contains supplementary material available at 10.1007/s00253-023-12556-7.