The complex lies on the overlapping trend of the Garibaldi and Pemberton volcanic belts, which were formed as a result of subduction zone magmatism along the Cascade Volcanic Arc in the last 29 million years. Two separate stages of magmatic activity have been identified at the Franklin Glacier Complex. The first magmatic stage about 6.8 million years ago involved the central emplacement of an elongated quartz monzonite stock. At least five porphyry and transitional vein-type mineral occurrences were deposited during this period. A series of smaller intrusions were emplaced during the second magmatic stage 2.2 to 3.9 million years ago, at least some of which appear to have been feeders for the overlying volcanic pile. The Franklin Glacier Complex is substantially older than the neighbouring Silverthrone Caldera to the northwest.