The control of grey squirrels (Sciurus carolinensis) is widely undertaken as a conservation measure to protect red squirrel (Sciurus vulgaris) populations in the UK. However, inconsistencies and omissions in data collection, as well as fluctuating financial resourcing of control efforts, have meant that it has to date proved difficult to quantify the impact of any regional control initiative upon populations. Here we have scrutinized a 13 years period (1998–2010) within an ongoing grey squirrel control project that reflects the resource challenges typically faced by red squirrel conservation programmes. We present evidence that despite variation in grey squirrel control intensity, the abundance of grey squirrels ultimately decreased significantly. Trapping success was significantly higher in spring and summer months and a greater abundance of grey squirrels was found in deciduous woodland and hazel dominated scrub relative to other habitats; two findings that reinforce existing guidance within national control best practice. Grey squirrels carry an infection that causes epidemic pathogenic disease if spread to the native red squirrel. We observed that the proportion of seropositive grey squirrels decreased constantly from 2003 to 2010 when only 4 % of sampled animals were seropositive. This discovery indicates that culling can in parallel remove both the competitive and disease threat posed to red by grey squirrels. The historical paucity of scientific data on the effectiveness of grey squirrel control as a tactic in UK red squirrel conservation means that the findings of this study will significantly advance conservation best practice and inform the development of future national strategy.