This paper deals with the design of an optimal stochastic controller possessing tracking capability of any reference output trajectory in the presence of measurement noise. We consider multi-input multi-output linear time-invariant systems and a proportional-integral-derivative (PID) controller. The system under consideration needs not be stable. A recursive algorithm providing optimal time-varying PID gains is proposed for the case where the number of inputs is larger than or equal to the number of outputs. The development of the proposed algorithm aims for per-time-sample minimisation of the mean-square output error in the presence of erroneous initial conditions, measurement noise, and process noise. Necessary and sufficient conditions are provided for the convergence of the output error covariance. In addition, convergence results are presented for discretised continuous-time plants. Simulation results are included to illustrate the performance capabilities of the proposed algorithm. Performance comparison with an optimal stochastic iterative learning control scheme, an optimal PID controller, an adaptive PID controller, and a recent optimal stochastic PID controller are also included.