The global rise of antibiotic resistance, particularly in critical pathogens such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacteriaceae, demands innovative therapeutic strategies. Despite their promise, conventional drug discovery pipelines remain slow, costly, and often ineffective. In contrast, antimicrobial peptides (AMPs) offer a compelling alternative due to their specificity, low resistance induction, and multifunctional activity, although their development is hindered by issues like poor stability and immunogenicity. To address these challenges, we introduce PANDORA (Peptide-based ANtimicrobial Design Optimized by Reinforcement Automation), an autonomous AI-driven platform for the optimized design of antibiotic peptides. PANDORA integrates predictive models (e.g., AMP activity, half-life, toxicity), generative transformer-based architectures for de novo sequence design, and explainable AI for property inference. All components are coordinated by a multi-agent reinforcement learning system that enables adaptive, end-to-end peptide engineering. Predictive models, fine-tuned on protein language embeddings with advanced feature extraction, reach classification accuracies above 90% for antimicrobial activity and >85% for toxicity risk estimation. Generative models, guided by physicochemical constraints, yield diverse candidate peptides with optimized therapeutic profiles. The platform supports natural language prompts and user-defined constraints, offering a flexible, user-friendly interface. Preliminary candidates are undergoing experimental validation against WHO-priority bacteria, with feedback used to further train the system via reinforcement learning. PANDORA represents a scalable, autonomous solution that fuses artificial intelligence, automation, and experimental validation. Its capacity to iteratively learn and adapt positions it as a transformative tool for accelerating peptide-based drug discovery in the fight against antibiotic resistance.