Standardised assays are often used to characterise aggression in animals. In ants, such assays can be applied at several organisational levels (e.g., colony, population) and at specific times during the season. However, whether the behaviour differs at these levels and changes over a few weeks remains largely unexplored. Here, six colonies from the high-elevation ant Tetramorium alpestre were collected weekly for five weeks from two behaviourally-different populations (aggressive and peaceful in intraspecific encounters). We conducted one-on-one worker encounters at the colony and population levels. When analysing the colony combinations separately, the behaviour was peaceful and remained so within the peaceful population; initial aggression became partially peaceful within the aggressive population; and initial aggression decreased occasionally and increased in one combination but remained constant for most across-population combinations. When analysing all colony combinations together, within-population behaviour remained similar, but across-population behaviour became peaceful. The observed behavioural differences among organisational levels emphasise the relevance of assessing both levels. Moreover, the effect of decreasing aggression is discernible already over a few weeks. Compression of the vegetation period at high elevations may compress such behavioural changes. Addressing both organisational levels and seasonality is important, particularly in studies of behavioural complexity such as in this ant. Display omitted •High-elevation ants were collected weekly for five weeks and aggression was tested.•Across-colony worker aggression changed over time depending on the colony combination.•Analysing two organisational levels (colony, population) revealed different results.•A shorter season in high elevation may accelerate a change in aggressive behaviour.•Organisational levels and seasonality should be considered in designing behavioural studies.