Breast cancer is the leading type of cancer. The triple negative is the most aggressive type of breast cancer, as it is resistant to several treatments as hormone based, for example. Cell metabolism is altered in cancer cells as they favor anaerobic pathways to produce energy in a faster pace and in accordance with the hypoxic environments found inside tumor mass, which is known as the Warburg effect. In this study, we sought to investigate the molecular mechanisms behind the different cell phenotypes during tumorigenesis. To pursue this goal, we employed proteomics in four types of cells; the non-tumorigenic epithelial cell MCF-10A, two triple negative breast cancer originated from primary tumor sites (MGSO-3 and MACL-1), and the metastatic tumor cell line MDA-231-MD. Our proteomic data shown that most proteins associated with the TCA cycle and oxidative phosphorylation (aerobic metabolic phase) were upregulated in primary cells while downregulated in metastatic cell, in line with a negative regulation of the Warburg effect for the primarily cells. We also shown that these cells have lower mitochondria density and upregulation of pro-apoptotic proteins when compared with metastatic cells. Molecular differences highlighted in this study may assist the scientific community in developing new protocols to treat the triple negative breast cancer.