Metagenomic sequencing is a promising approach for identifying and characterizing organisms and their functional characteristics in complex, polymicrobial infections, such as airway infections in people with cystic fibrosis. These analyses are often hampered, however, by overwhelming quantities of human DNA, yielding only a small proportion of microbial reads for analysis. In addition, many abundant microbes in respiratory samples can produce large quantities of extracellular bacterial DNA originating either from biofilms or dead cells. We describe a method for simultaneously depleting DNA from intact human cells and extracellular DNA (human and bacterial) in sputum, using selective lysis of eukaryotic cells and endonuclease digestion. We show that this method increases microbial sequencing depth and, consequently, both the number of taxa detected and coverage of individual genes such as those involved in antibiotic resistance. This finding underscores the substantial impact of DNA from sources other than live bacteria in microbiological analyses of complex, chronic infection specimens. Display omitted •Human and extracellular bacterial DNA can bias metagenomic sequencing•Hypotonic lysis, endonuclease digestion limit human and extracellular bacterial DNA•Reducing extracellular DNA optimizes metagenomic sequencing of viable bacterial cells•Increased microbial sequencing coverage improves detection of important genes Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.