Through recurrent structural reform programmes governments are on a quest to design public organizations that will stand the test of their environment. One of the approaches to uncertain or sensitive issues has been to create various forms of (semi‐)autonomous organizations with substantial strategic discretion. However, while governments repeatedly experiment with designs, one might simultaneously expect that such interference through repeated structural change may limit the degree of strategic policy autonomy perceived by senior managers. More specifically, we propose that intense structural reforms may inadvertently reduce strategic policy autonomy perceptions through two mechanisms. First, intense sequences of structural reforms may lead to perceptions of relatively controlling political principals. Second, they may reduce an organization’s ability to accrue resources beneficial to autonomy, such as a strong internal culture, network embeddedness and expertise. Results indicate that strategic policy autonomy perceptions will indeed be detrimentally affected for organizations that experience intense sequences of structural reform.