Flexible manufacturing cells provide significant advantages in low-volume mass-customization production but also induce added complexity and technical challenges in terms of integration, control, and extensibility. The variety of closed-source industrial protocols, the heterogeneous equipment, and the product’s manufacturing specifications are main points of consideration in the development of such a system. This study aims to describe the approach, from concept to implementation, for the development of the controller for a flexible manufacturing cell consisting of heterogeneous equipment in terms of functions and communication interfaces. Emphasis is put on the considerations and challenges for effective integration, extensibility, and interoperability. Scheduling and monitoring performed by the developed controller are demonstrated for a manufacturing cell producing microfluidic devices (bioMEMS) that consists of six workstations and a robot-based handling system. Communication between the system controller and the workstations was based on open-source technologies instead of proprietary software and protocols, to support interoperability and, to a considerable extent, code reusability.