The consumption of fermented foods has gained considerable attention due to the ability to deliver live microbes with specific enzymatic activities, and fermentation metabolites, which might play a role in health promotion or disease prevention. The aim of this study was to determine the impact of long-term daily consumption of a high-protein drained yoghurt (Skyr) on intestinal microbial ecology and fermentation activity in a free-living cohort of overweight and obese women (n = 29). Longitudinal analysis and quantitative microbiota profiling identified time intervals with significantly differentially abundant taxa during intervention that differed in functional activity. Our results suggest that ingestion of Skyr persistently modified intestinal microbial cross-feeding activities which altered fecal short chain fatty acid profiles. This study provides a framework indicating the potential of fermented dairy containing starter cultures, lactose and lactate in individualized nutrition or microbiome engineering due to nutritive and microbial components.