The traditional aviary decontamination process involves farmers applying pesticides to the aviary’s ground. These agricultural defenses are easily dispersed in the air, making the farmers susceptible to chronic diseases related to recurrent exposure. Industry 5.0 raises new pillars of research and innovation in transitioning to more sustainable, human-centric, and resilient companies. Based on these concepts, this paper presents a new aviary decontamination process that uses IoT and a robotic platform coupled with ozonizer (O₃) and ultraviolet light (UVL). These clean technologies can successfully decontaminate poultry farms against pathogenic microorganisms, insects, and mites. Also, they can degrade toxic compounds used to control living organisms. This new decontamination process uses physicochemical information from the poultry litter through sensors installed in the environment, which allows accurate and safe disinfection. Different experimental tests were conducted to construct the system. First, tests related to measuring soil moisture, temperature, and pH were carried out, establishing the range of use and the confidence interval of the measurements. The robot’s navigation uses a back-and-forth motion that parallels the aviary’s longest side because it reduces the number of turns, reducing energy consumption. This task becomes more accessible because of the aviaries’ standardized geometry. Furthermore, the prototype was tested in a real aviary to confirm the innovation, safety, and effectiveness of the proposal. Tests have shown that the UV + ozone combination is sufficient to disinfect this environment.