Nowadays, small and medium sized enterprises (SMEs) are becoming increasingly competitive. In order to fulfill the rapidly changing market and diversified demands of customers, the SMEs need to achieve and maintain high productivity and quality, with fast response, sufficient flexibility, and short lead times. Therefore, Industry 4.0 offers various manufacturing paradigms that might be a solution in order to increase the productivity of SMEs such as intelligent and flexible manufacturing. Furthermore, in the last decade, the emphasis on adopting eco-friendly practices, implementing sustainability measures, and protecting the environment has continued to grow, to gain traction across SMEs. In fact, because of this need, many SMEs are now adopting sustainable manufacturing practices in response to this increased focus on sustainability and environmental stewardship. The main purpose of this paper is to design and study the implementation of a sustainable, intelligent material handling system for material distribution with utilizing an agent-based algorithm as control architecture. A time study-based methodology has been implemented to evaluate the overall equipment effectiveness (OEE) to identify the matters that need to be resolved and optimized to increase the OEE percentage with consideration of the sustainability of the system. An exhaustive analytical trend applied to the generated time study data. Accordingly, further hardware, software, and layout design limitation and problems detected, and the proper solutions were anticipated. The observed time study results were presented, a fundamental set of analytical observation and information with associated histograms was reviewed. In addition, the study aims to recognize and analyze effective factors on the sustainability of improved processes, using a simple model. To do this, using experts’ viewpoints, affective factors on the sustainability of process improvement activities are determined.