The pathogenesis of brucellosis depends on the ability of bacteria from the genus Brucella to invade and replicate within animal cells. To understand the molecular pathways used by Brucella spp. to reach its intracellular niche, robust and reproducible bacteria purification protocols that provide enough material for biochemical and molecular biology studies are essential. Here, we describe a detailed methodology designed to extract and purify viable brucellae from mammalian host cells at different time periods of their intracellular cycle. The yield of proteins and nucleic acids is sufficient to perform immunochemical analysis, genetic studies, transcriptomics, and proteomics among others.