Embedded controllers for multivariable processes have become a powerful tool in industrial implementations. Here, the Model Predictive Control offers higher performances than standard control methods. However, they face low computational resources, which reduces their processing capabilities. Based on pipelining concept, this paper presents a new embedded software-based implementation for a constrained Multi-Input-Multi-Output predictive control algorithm. The main goal of this work focuses on improving the timing performance and the resource usage of the control algorithm. Therefore, a profiling study of the baseline algorithm is developed, and the performance bottlenecks are identified. The functionality and effectiveness of the proposed implementation are validated in the NI myRIO 1900 platform using the simulation of a jet transport aircraft during cruise flight and a tape transport system. Numerical results for the study cases show that the latency and the processor usage are substantially reduced compared with the baseline algorithm, 4.6× and 3.17× respectively. Thus, efficient program execution is obtained which makes the proposed software-based implementation mainly suitable for embedded control systems.