Tuberculosis (TB) is currently the number one killer among infectious diseases worldwide and M. tuberculosis is the leading agent. Lipids are abundant molecules during the infectious cycle of M. tuberculosis and some studies suggest that host lipids play a role in the dormancy and drug tolerance of M. tuberculosis. In vitro models of dormant mycobacteria better mimicking its actual metabolic state during pathogenesis are needed. Though most studies have focused on the mycobacterial lipid metabolism under standard culture conditions, little is known about the transcriptome of M. tuberculosis in a lipid environment. In this study, the transcriptome of M. tuberculosis H37Rv in a lipid-rich dormancy model was determined, under aerobic and hypoxic conditions, using RNAseq. Transcriptomic results were confirmed by the gold standard, qRT-PCR and transcriptomics results were linked to the mycobacterial phenotype through a drug susceptibility test (DST). Lipids significantly induced the expression of 368 genes. A main core lipid response was observed involving detoxification systems, efflux pumps and ABC transport systems as well as systems for iron caption and sulfur reduction. In co-expression with non-coding RNAs that may act coordinately to prepare the machinery conferring drug tolerance and increasing a persistent population. Additionally, to confirm a phenotype of drug tolerance, the susceptibility of M. tuberculosis was tested in the lipid-rich dormancy model, to two antibiotic combinations: rifampicin, moxifloxacin, amikacin and metronidazole (RIF-MXF-AMK-MTZ), and rifampicin, moxifloxacin, amikacin and pretomanid (RIF-MXF-AMK-PA). Although their effectiveness in in vitro cultures with dextrose as carbon source have been proved, we observed that none of the antibiotic mixtures were bactericidal in the presence of lipids. The presence of lipids as carbon source may confer tolerance to M. tuberculosis against the mixture of antibiotics tested, which could be even higher during dormant stages. Results of this study suggest that this phenotype is helped by detoxification systems, involving iron caption and sulfur reduction systems. Findings of this study could be useful to tag relevant pathways for the development of new drugs, vaccines and new strategies to control TB. Additionally, implementation of lipids in DST on clinical isolates could potentially lead to a better treatment strategy.