This paper investigates the problem of global output feedback tracking control of flexible joint robots. Despite the fact that only link position and actuator position are available from measurements, the proposed controller ensures that the link position globally tracks the desired trajectory while keeping all the remaining signals bounded. The controller development uses a partial state-feedback linearization technique combined with the integrator backstepping control design method whereas a filter and an observer are utilized to remove the requirement of link and actuator velocity measurements. Partial state-feedback linearization of robot dynamics is performed by factoring the manipulator mass matrix into a quadratic form involving an integrable root matrix. The applicability of the proposed general design methodology is illustrated by an example of flexible joint planar robots. Numerical results for a two-link flexible joint planar robot are also provided.