Protonic ceramic fuel cells (PCFCs) show great promise as a technology for clean power generation. However, the sluggish reaction kinetics and instability of the cathodes continue to impede their commercialization. Here, we report a multiphase nanocomposite produced through dual self-assembly, which serves as a highly active and durable cathode for PCFCs. During cathode sintering, self-assembly takes place to create a composite consisting of PrNi0.5Co0.5O3-δ(PNC), BaCe0.7Zr0.1Y0.2O3-δ(BCZY), and PrOxnanoparticles. Compared to the single-phase PNC cathode, this cathode demonstrates enhanced performance with a reduction of 49.1% in ohmic resistance and 48.5% in polarization resistance at 700 °C. This outcome is attributed to improved oxygen surface exchange kinetics and electrolyte–cathode interface strength. Furthermore, the self-assembled cathode in the single cell exhibits a 33.3% increase in power output relative to that of the PNC cathode cell. More interestingly, the cell displays performance activation during 400 h of operation, resulting in a power output increase of 27.5%. The cathode is revealed to be further self-assembled during operation in the post-mortem analysis, featuring an in situ-formed needle-like nanocomposite composed of BaPrO3and BCZY. This work presents an innovative approach to nanocomposite self-assembly for potential use in PCFC cathode applications.