The combination of different ”omics” approaches, such as genomics and proteomics, is necessary to give a detailed and complete insight into microbiome comprehension. For example, genomic analyses provide information on the composition of a microbiome, and proteomic analyses provide information on the activity of microorganisms. The proper sample collection, sample preparation, and accurate analytical methods play a crucial role in generating reliable data. In a previous work, we have developed a ChipFilter device for proteomic analysis of microbial samples. We have shown that this device coupled to LC-MS/MS can successfully be used for the identification of microbial proteins. We have shown that it is possible to directly lyse the cells and digest the proteins in the ChipFilter to allow a higher number of proteins and peptides identification than standard protocols, even at low cell density. In the present work, we have developed our workflow to analyze both proteins and nucleic acids from the same sample. Using cultures of E. coli, B. subtilis, and S. cerevisiae, we performed lysis and proteolysis in the device. After peptide recovery and analysis, DNA from the same samples was recovered and successfully amplified by PCR for the 3 species. This workflow was used on a complex mixture of known compositions. Protein analysis was carried out, enabling the identification of proteins from 16 out of the 17 species making up this standard, leading to the identification of more than 2000 proteins. DNA was recovered and analyzed by NGS, with performances comparable to that of DNA extracted with a commercial kit without proteolysis. Our results show that the Chipfilter device can be used to prepare samples for proteomic and genomic analyses. This is particularly interesting for reducing sampling bias and in the case of precious samples