Protostellar jets and outflows are key features of the star-formation process, and primary processes of the feedback of young stars on the interstellar medium. Understanding the underlying shocks is necessary to explain how jet and outflow systems are launched, and to quantify their chemical and energetic impacts on the surrounding medium. We performed a high-spectral resolution study of the [OI]63um emission in the outflow of the intermediate-mass Class 0 protostar Cep E-mm. The goal is to determine the structure of the outflow, to constrain the chemical conditions in the various components, and to understand the nature of the underlying shocks, thus probing the origin of the mass-loss phenomenon. We present observations of the OI ^3^P_1_ -> ^3^P_2_, OH between ^2^{Pi}_1/2_ J=3/2 and J=1/2 at 1837.8GHz, and CO (16-15) lines with the GREAT receiver onboard SOFIA towards three positions in the Cep E protostellar outflow: Cep E-mm (the driving protostar), Cep E-BI (in the southern lobe), and Cep E-BII (the terminal position in the southern lobe).