In this paper, a new technique is proposed for trajectory tracking of a flexible spacecraft subject to angular velocity constraints. The problem is addressed using an output to input saturation transformation (OIST) which converts the prescribed bounds into state-dependent saturations on the control input signals. It is shown that an interval observer can be used in combination with the OIST technique to ensure that the constraints remain satisfied despite unmeasured flexible modes and torque disturbances. Some realistic simulations conclude the paper and validate our approach.