Our study aimed to evaluate changes in the epidemiology of pathogens causing surgical site infections (SSIs) in England between 2000 and 2013 in the context of intensified national interventions to reduce healthcare-associated infections introduced since 2006. National prospective surveillance data on target surgical procedures were used for this study. Data on causative organism were available for 72% of inpatient-detected SSIs meeting the standard case definitions for superficial, deep and organ-space infections (9767/13 531) which were analysed for trends. A multivariable logistic linear mixed model with hospital random effects was fitted to evaluate trends by pathogen. Staphylococcus aureus was the predominant cause of SSI between 2000 (41%) and 2009 (24%), decreasing from 2006 onwards reaching 16% in 2013. Data for 2005–2013 showed that the odds of SSI caused by S. aureus decreased significantly by 14% per year [adjusted odds ratio (aOR) 0·86, 95% confidence interval (CI) 0·83–0·89] driven by significant decreases in methicillin-resistant S. aureus (MRSA) (aOR 0·71, 95% CI 0·68–0·75). However a small significant increase in methicillin-sensitive S. aureus was identified (aOR 1·06, 95% CI 1·02–1·10). Enterobacteriaceae were stable during 2000–2007 (12% of cases overall), increasing from 2008 (18%) onwards, being present in 25% of cases in 2013; the model supported these increasing trends during 2007–2013 (aOR 1·12, 95% CI 1·07–1·18). The decreasing trends in S. aureus SSIs from 2006 and the increases in Enterobacteriaceae SSIs from 2008 may be related to intensified national efforts targeted at reducing MRSA bacteraemia combined with changes in antibiotic use aimed at controlling C. difficile infections.