Millions of mice are used every year for scientific research, representing the majority of scientific procedures conducted on animals. The standard method used to pick up laboratory mice for general husbandry and experimental procedures is known as tail handling and involves the capture, elevation and restraint of mice via their tails. There is growing evidence that, compared to non-aversive handling methods (i.e. tunnel and cup), tail handling increases behavioural signs of anxiety and induces anhedonia. Hence tail handling has a negative impact on mouse welfare. Here, we investigated whether repeated scruff restraint, intraperitoneal (IP) injections and anaesthesia negated the reduction in anxiety-related behaviour in tunnel compared with tail handled BALB/c mice. We found that mice which experienced repeated restraint spent less time interacting with a handler compared to mice that were handled only. However, after repeated restraint, tunnel handled mice showed increased willingness to interact with a handler, and reduced anxiety in standard behavioural tests compared with tail handled mice. The type of procedure experienced (IP injection or anaesthesia), and the duration after which behaviour was measured after a procedure affected the willingness of mice to interact with a handler. Despite this, compared with tail handling, tunnel handling reduced anxiety in standard behavioural tests and increased willingness to interact with a handler within hours after procedures. This suggests that the welfare benefits of tunnel handling are widely applicable and not diminished by the use of other putatively more invasive procedures that are frequently used in the laboratory. Therefore, the simple refinement of replacing tail with tunnel handling for routine husbandry and procedures will deliver a substantial improvement for mouse welfare and has the potential for improving scientific outcomes.