Veterinary practices can be stressful places for dogs. Decreasing stress during veterinary consultations is therefore a major concern, since animal welfare matters both for owners and veterinarians. Stress can be expressed through behaviour modifications; monitoring canine behaviour is thus one way to assess stress levels. We also know that the owner can affect dog behaviour in different ways. The aim of this study was therefore to assess the effect of the presence of owners on the behaviour of their dogs in veterinary consultations. We studied 25 dog-owner dyads at two standardised veterinary consultations, conducted at intervals of 5–7 weeks; the owner was present for the first consultation and absent for the second (O/NoO group, n = 12), or vice versa (NoO/O group, n = 13). A consultation consisted in three phases: exploration, examination, greeting. Dog behaviours were compared between the two conditions using a video recording. Despite some limitations (e.g. no male owners, the exclusion of aggressive dogs, a limited sample size, minimally invasive veterinary examinations, restricted owner-dog interactions), our results showed that the presence or absence of the owner had no significant effect on the stress-related behaviour of the dog or the veterinarian's ability to handle the animal during the examination phase (P > 0.05). Nevertheless, the behaviour of the dogs towards people was affected before, during, and after the veterinary examination. In the presence of their owner, dogs were more willing to enter the consultation room (P < 0.05), and they appeared more relaxed during the exploration phase (P < 0.01). During the examination, dogs looked in direction of their owner in both situations (owner present and behind the door, respectively; P < 0.001). These results suggest that allowing the owner to stay in the room during veterinary consultations is a better option for canine welfare.