The simultaneous detection of carcinoembryonic antigen (CEA) and microRNA-21 (miR-21) is of significant clinical importance for cancer diagnosis, prognosis evaluation, and therapy monitoring. In this study, we developed a novel electrochemical biosensor utilizing a peptide-self-assembly-engineered signal amplification (PSA-e-SA) nanoarchitectonic strategy to achieve ultrasensitive and simultaneous quantification of these two critical biomarkers. By designing amphiphilic peptides (C₁₆-MB-Aptamer_CEA and C₁₆-Fc-ssDNA2) as multifunctional probes, the system exploits their dual roles in target recognition and signal amplification. These peptides self-assemble into nanostructures under mild conditions, facilitating enhanced loading of electroactive molecules such as methylene blue (MB) and ferrocene (Fc), thereby significantly amplifying the electrochemical signal. The biosensor achieved detection limits of 0.788 pM for CEA and 0.0357 nM for miR-21, demonstrating remarkable sensitivity enhancements of 18-fold and 3.8-fold compared to unamplified approaches. As a proof-of-concept study, further experiments underscored the excellent reproducibility and stability of the strategy while also demonstrating its applicability when tested with simulated serum samples. Thus, this work not only presents a valuable assay tool for early cancer diagnosis and biomarker analysis but also indicates that this signal amplification strategy based on peptide self-assembly engineering can be extended to detect other disease-related biomarkers, propelling the development of clinical applications for multifunctional biosensors.