The decrease in the cost of sensors during the last years, and the arrival of the 5th generation of mobile technology will greatly benefit Internet of Things (IoT) innovation. Accordingly, the use of IoT in new agronomic practices might be a vital part for improving soil quality, optimising water usage, or improving the environment. Nonetheless, the implementation of IoT systems to foster environmental awareness in educational settings is still unexplored. This work addresses the educational need to train students on how to design complex sensor-based IoT ecosystems. Hence, a Project-Based-Learning approach is followed to explore multidisciplinary learning processes implementing IoT systems that varied in the sensors, actuators, microcontrollers, plants, soils and irrigation system they used. Three different types of planters were implemented, namely, hydroponic system, vertical garden, and rectangular planters. This work presents three key contributions that might help to improve teaching and learning processes. First, a holistic architecture describing how IoT ecosystems can be implemented in higher education settings is presented. Second, the results of an evaluation exploring teamwork performance in multidisciplinary groups is reported. Third, alternative initiatives to promote environmental awareness in educational contexts (based on the lessons learned) are suggested. The results of the evaluation show that multidisciplinary work including students from different expertise areas is highly beneficial for learning as well as on the perception of quality of the work obtained by the whole group. These conclusions rekindle the need to encourage work in multidisciplinary teams to train engineers for Industry 4.0 in Higher Education.