Researchers have argued that political parties in government matter for policy integration reforms, but the way they do so remains somewhat undetermined. In this paper, we contribute to this literature by tackling two interrelated open questions: How does the presence of different political parties in government, which rely on policy programs on opposite sides of the ideological spectrum, shape the intensity of policy integration reforms? To what extent do changes in governing political parties affect the political motivation of policy integration reforms and thereby influence the goals and means of these reforms? To explore these questions, we examine a case where institutional capacity is generally favorable to such reforms. Specifically, we compare policy integration reforms in the UK under the New Labor government (1997–2010) with those passed by the Conservative governments (1979–1996), and by the coalition government of Conservatives and Liberal Democrats (2010–2014). We find that political parties’ policy positions, and respectively, their political motivations, decisively shape the intensity of policy integration reforms, as well as their substantial goals and means. Furthermore, our results imply that changes in governing parties increase the overall frequency but can reduce the coherence of reform programs over time. These results point to a paradox for the governance of problems through policy integration, whereby the presence of high institutional capacity as provided by a majoritarian system can have negative long-term consequences for policies aiming to solve complex problems.