Background An essential component in the development of a sustainable pig production is the reduction of nitrogen excretion in fattening pigs. Pig feeds typically contain high levels of dietary crude protein, and due to incomplete conversion to muscle tissue, excess nitrogen is excreted, resulting in environmental problems such as nitrate pollution and greenhouse gas emissions. Therefore, improving protein efficiency (PE), i.e. the proportion of dietary protein that remains in the carcass and is thus available for meat production, is desirable. This study aimed to estimate the heritability (h2) of PE and its genetic correlations with phosphorus efficiency, three performance, seven meat quality and two carcass quality traits when pigs were fed a 20% protein-restricted diet, using a total of 1,071 Swiss Large White pigs. To determine PE, the intake of feed with known nutrient content was accurately recorded for each pig and the nitrogen and phosphorus content of the carcass was determined using dual-energy X-ray absorptiometry. Genetic analysis was performed with a Bayesian animal model. Results We found an average PE of 0.39 ± 0.04 and a heritability of 0.43 (0.29, 0.58). PE showed a low genetic correlation with phosphorus efficiency (0.12 [0.04, 0.21]) and moderate genetic correlations with feed conversion ratio (−0.40 [-0.50, -0.30]), average daily gain (−0.34 [-0.41, -0.23]) and average daily feed intake (−0.61 [-0.69, -0.50]). The genetic correlations between PE and meat quality traits were not significantly different from zero except for meat redness (−0.40 [-0.58, -0.09]) and meat yellowness (−0.27 [-0.45, -0.04]). In contrast, feed conversion ratio showed unfavourable genetic correlations with meat colour, drip loss and cooking loss. Conclusions Protein efficiency is heritable and can be considered in breeding to reduce the environmental impact of pig production without influencing meat quality traits, but the potential for coselecting improved phosphorus efficiency is rather small. Selecting nutrient efficiencies might be a more suitable strategy to reduce nitrogen pollution from manure than focusing on FCR because the latter shows genetic antagonism with meat quality in our population.