The debate on the use of chimpanzees (Pan troglodytes) in biomedical research has been ongoing for several years now. In 2012, the decision was made to retire a large number of laboratory chimpanzees in the United States of America. Relocation of these animals to sanctuaries, rescue centres, and zoos involve several changes in environment and husbandry routines. Because these animals often have a history of maternal deprivation, and consequently may suffer from an increased sensitivity to stress, these management changes may affect their behaviour. In The Netherlands, six groups of adult chimpanzees (n = 28), which were removed from their mother when juvenile and were hand or peer reared, were relocated from a biomedical laboratory to substantially larger enclosures at a Dutch sanctuary. This sanctuary applied different animal management routines. It was studied whether long-term agonistic, affiliative, and abnormal behaviour was affected by the relocation and alteration in behavioural management. The chimpanzees’ behaviour was observed at the laboratory and during four years at the sanctuary, which resulted in 309 h of observational data. Results indicated that the chimpanzees performed more allogrooming and less aggressive interactions at the sanctuary compared to the laboratory. However, abnormal behaviour was performed more often at the sanctuary. These results suggest that additional measures should be taken to enhance the welfare level of chimpanzees, at least for those that have a history of maternal deprivation.