Integrated photonics in trapped-ion systems are critical for the realization of applications such as portable optical atomic clocks and scalable quantum computers. However, system-level integration of all required functionalities remains a key challenge. In this work, we demonstrate an autonomously operating optical clock having a short-term frequency instability of 3.14(5)×10^-14/√τ using an ensemble of four 171Yb+ ions trapped in a multi-site surface-electrode trap at room temperature. All clock operations are performed with light delivered via on-chip waveguides. We showcase the system’s resilience through sustained, autonomous operation featuring automated ion shuttling and reloading to mitigate ion loss during interleaved clock measurements. This work paves the way beyond component-level functionality to establish a viable and robust architecture for the next generation of portable, multi-ion quantum sensors and computers.