This longitudinal study examines the impact of office type on employees’ perception of managers’ leadership behaviours, which is an unexplored area. The expanding research related to activity-based flexible offices (AFOs) has mainly focused on employees’ working conditions and health outcomes, not on the changes in leadership behaviours when moving from traditional offices to AFOs. Office workers (n = 261) from five office sites within a large Swedish government agency were included in a controlled study of a natural intervention. At four sites, traditional offices were replaced by AFOs, while workers at one site with no relocation acted as the control. The same employees rated different leadership behaviours in a web-based questionnaire at baseline and at one follow-up. The analyses showed that relocations from cell and open-plan offices to AFOs were clearly related to a decrease in the perception of relation-oriented leadership behaviours. However, coming from open-plan offices to AFOs also decreased the perception of the other leadership dimensions. As expected, the control group was stable over time in their perceptions. This emphasises the need for organisations to provide managers with prerequisites so they can keep up with behaviours that support employees’ performance and health when office designs and ways of working are changed.