Modern industrial automation supported by Cyber–Physical Systems (CPSs) requires high flexibility, which is achieved through increased interconnection between modules. This interconnection introduces a layer of symmetry into the design and operation of CPSs, balancing the distribution of tasks and resources across the system and streamlining the flow of information. However, this adaptability also exposes control systems to security threats, particularly through novel communication links that are vulnerable to cyberattacks. Traditional strategies may have limitations in these applications. This research proposes a design approach for control applications supported by CPSs that incorporates cyberattack detection and tolerance strategies. Using a modular and adaptive approach, the system is partitioned into microservices for scalability and resilience, allowing structural symmetry to be maintained. Schedulability assessments ensure that critical timing constraints are met, improving overall system symmetry and performance. Advanced cyberattack detection and isolation systems generate alarms and facilitate rapid response with replicas of affected components. These replicas enable the system to recover from and tolerate cyberattacks, maintaining uninterrupted operation and preserving the balanced structure of the system. In conclusion, the proposed approach addresses the security challenges in CPS-based control applications and provides an integrated and robust approach to protect industrial automation systems from cyber threats. A case study conducted at a juice production facility in Colima, México, demonstrated how the architecture can be applied to complex processes such as pH control, from simulation to industrial implementation. The study highlighted a plug-and-play approach, starting with component definitions and relationships, and extending to technology integration, thereby reinforcing symmetry and efficiency within the system.