The structure and organisation of the machinery of government are key to the ambitions of political coalitions. When portfolio allocation and agencification are a function of political choice, political volatility should also affect the internal structure of government administrations. This study tests the effects of political turnover of individual ministers and of the political ideology of coalitions on a dataset of intra-ministerial changes in Dutch ministries between 1980 and 2014. Findings indicate that the turnover of political heads of departments and the shifts in policy preferences between successive coalitions indeed affects the internal structure of ministerial departments. Political variables have a strong impact, particularly changes in the left-right position of the government. A clear pattern for how precisely politics affect the structural design of public organisations remains absent, in spite of the robustness of the findings. Most ministries experience significant effect of executive turnover, sometimes increasing the hazards of intra-organisational transitions and sometimes increasing stability. It turns out that ministers can substantially rearrange their organisations in line with their policy preferences but do not necessarily do so. Sometimes the effect of liberal ideology dominates, sometimes the effect of the policy preferences with respect to a specific domain prevails.