The organizational configuration reflects the specialty configuration in IPU. The configuration is divided into the same specialties as the corresponding collaborating DTU departments.

Some of the major collaborations, which have shaped the specialty configuration, are the collaborations with the DTU departments: the Department of Manufacturing Engineering and Management (IPL), the Department of Mechanical Engineering (MEK), and the Technical Knowledge Center of Denmark (DTV); all of which are organized into sections within IPU. The names of the sections are: IPU-Product Development, IPU-Production, and IPU-Information.

Some of the other collaborations are with BioCentrum, the Department of Chemical Engineering, and the Department of Informatics and Mathematical Modelling, all organized in IPU-Venture.

Subsidiary companies are Arcanic A/S in collaboration with DTV.

Involvement in association activities is done in collaboration with IPL in ATV-Semapp and in collaboration with the Department of Mechanical Engineering, The Mechatronics Association and Fluid Power Net International, and the Danish Simulation Association (Dansk Simuleringsforening).