Until now extrusion is not applied for pharmaceutical encapsulation processes, whereas extrusion is widely used for encapsulation of flavours within food applications. Based on previous mixing studies, a hot melt counter-rotating extrusion process for encapsulation of liquid active pharmaceutical ingredients (APIs) was investigated. The mixing ratio of maltodextrin to sucrose as matrix material was adapted in first extrusion trials. Then the number of die holes was investigated to decrease expansion and agglutination of extrudates to a minimum. At a screw speed of 180 min−1 the product temperature was decreased below 142 °C, resulting in extrudates of cylindrical shape with a crystalline content of 9–16%. Volatile orange terpenes and the nonvolatile α-tocopherol were chosen as model APIs. Design of experiments were performed to investigate the influences of barrel temperature, powder feed rate, and API content on the API retentions. A maximum of 9.2% α-tocopherol was encapsulated, while the orange terpene encapsulation rate decreased to 6.0% due to evaporation after leaving the die. During 12 weeks of storage re-crystallization of sucrose occurred; however, the encapsulated orange terpene amount remained unchanged.