We experimentally demonstrate the active control of a plasmonic metamaterial operating in the quantum regime. A two-dimensional metamaterial consisting of unit cells made from gold nanorods is investigated. Using an external laser, we control the temperature of the metamaterial and carry out quantum process tomography on single-photon polarization-encoded qubits sent through, characterizing the metamaterial as a variable quantum channel. The overall polarization response can be tuned by up to 33% for particular nanorod dimensions. To explain the results, we develop a theoretical model and find that the experimental results match the predicted behavior well. This work goes beyond the use of simple passive quantum plasmonic systems and shows that external control of plasmonic elements enables a flexible device that can be used for quantum state engineering.