The influence of the human microbiome on health is an important area of ongoing investigation for medicine and diagnostics. For these studies it is crucial to have a reliable, reproducible extraction method which is able to extract DNA of all microorganisms with comparable efficiency, while simultaneously depleting inhibitory substances which might disturb subsequent downstream analysis. We present the results of DNA extraction and microbiome analysis from stool, saliva, and a variety of swabs (buccal, vaginal, rectal, skin) using the DNeasy PowerSoil Pro/QIAamp PowerFecal Pro kits, including automation options and process handling improvements.