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Abstract Semiconductor microcavities with a high quality‐factor are an important component for photonics research and technology, especially in the strong coupling regime. While van der Waals semiconductors have emerged as an interesting platform for photonics due to their strong exciton–photon interaction strength and engineering flexibility, incorporating them in photonic devices requires heterogeneous integration and remains a challenge. This study demonstrates a method to assemble high quality factor microcavities for van der Waals materials, using high reflectance top mirrors which, similar to van der Waals materials themselves, can be nondestructively and reliably peeled off the substrate and transferred onto the rest of the device. Microcavities are created with quality factors consistently above 2000 and up to 11000 ± 800; and the strong coupling regime is demonstrated. The method can be generalized to other types of heterogeneously integrated photonic structures and will facilitate research on cavity quantum electrodynamic and photonic systems using van der Waals materials.