This article aims to explain the under-researched phenomenon of why the European Commission (the Commission), as ‘guardian of the Treaties’, tolerates member states’ noncompliance with the EU law. While major accounts of selective enforcement depict the Commission as a self-serving political entrepreneur, this paper assumes that it is a trustee guardian of EU treaties that aims to safeguard the stability and integrity of the EU legal order. For this purpose, the Commission is theorized to strategically utilize toleration of noncompliance to evade jurisdiction overlap and norm collision. Relying on the detailed tracing of the Commission's enforcement leniency towards Slovakia regarding pharmaceutical parallel trade, this illustrative case study indicates that toleration of noncompliance is a necessary evil for the Commission and other stakeholders to navigate through a legal and political impasse. And it simultaneously preserves the delicate integrity of the existing legal order of EU free movement law.