Hierarchical control architectures are a common approach when hydraulic systems are under study; provided their multi-domain nature, the control scheme is commonly split into different hierarchical levels each one associated with a particular physical domain. This paper presents the application of a model-based control structure called Embedded Model Control (EMC) when a hierarchical scheme is implemented on an electro-hydraulic proportional valve. The overall control consists of two hierarchical loops: the inner loop is the solenoid current regulator with a closed loop bandwidth close to 1kHz. The outer loop is a position tracking control, in charge of the accurate positioning of the spool with respect to valve openings. The paper addresses the outer loop, i.e., the tracking of mechanical spool position by using the EMC. Analysis and synthesis are presented as well as experimental results obtained from a test rig provided by an industrial manufacturer. •The outer loop of a hierarchical controller for proportional valves is designed by using the Embedded Model Control.•Design is supported by a discrete-time embedded model obtained from experimental data.•Parametric uncertainty and neglected dynamics are addressed by disturbance estimation and cancelation through the control law.•Experimental results show that the demanding requirements are achieved by the implementation of the EMC framework.