Nanoparticle encapsulation inside zirconium-based metal-organic frameworks (NP@MOF) is hard to control, and the resulting materials often have nonuniform morphologies with NPs on the external surface of MOFs and NP aggregates inside the MOFs. In this work, we report the controlled encapsulation of gold nanorods (AuNRs) by a scu-topology Zr-MOF, via a room-temperature MOF assembly. This is achieved by functionalizing the AuNRs with poly(ethylene glycol) surface ligands, allowing them to retain colloidal stability in the precursor solution and to seed the MOF growth. Using this approach, we achieve core-shell yields exceeding 99%, tuning the MOF particle size via the solution concentration of AuNRs. The functionality of AuNR@MOFs is demonstrated by using the AuNRs as embedded probes for selective surface-enhanced Raman spectroscopy (SERS). The AuNR@MOFs are able to both take-up or block molecules from the pores, thereby facilitating highly selective sensing at the AuNR ends. This proof-of-principle study serves to present both the outstanding level of control in the synthesis and the high potential for AuNR@Zr-MOF composites for SERS.