Endochin-like quinolones (ELQ) are highly potent inhibitors of the Toxoplasma gondii cytochrome bc1 complex, the third complex of the mitochondrial electron transport chain. We evaluated differential gene expression of type 1 (RH) and type 2 (ME49) T. gondii treated with ELQ-316 using RNA sequencing at multiple time points over 4 and 10 days, respectively. The transcriptional response to ELQ-316 substantially differed over time and across the two strains. Between 24 hours and 96 hours of ELQ-316, ME49 undergoes a marked shift in gene expression compared to RH. Much of the difference in strain response appears to be attributable to in vitro bradyzoite differentiation and cyst formation in ME49. At 96 hours, 439 genes in ME49 were upregulated more than 4-fold, compared to 373 genes in RH. Of the upregulated genes, only 165 were common between the two strains, demonstrating unique gene expression responses to ELQ-treatment between strains. In ME49, 107 of 190 bradyzoite-associated genes (upregulated in multiple other bradyzoite RNAseq datasets) were upregulated at 96 hours, including BAG1, Enolase 1, LDH2, and AP2IX-9. In RH, 49 bradyzoite-associated genes were upregulated, and typical bradyzoite signatures were not. All changes in transcription in ME49 were not explained by bradyzoite transformation. In ME49 and RH, 351 and 324 genes non-bradyzoite-associated genes, respectively, were upregulated under ELQ-treatment: less than half of these genes were common between strains. Analysis of metabolic pathways and transcriptional regulation in response to cytochrome bc1 inhibition provides insight into mechanisms of T. gondii adaptation and key differences between strains.