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Abstract The colonization of biomedical surfaces by bacterial biofilms is concerning because these microorganisms display higher antimicrobial resistance in biofilms than in liquid cultures. Developing antimicrobial coatings that can be easily applied to medically‐relevant complex‐shaped objects, such as implants and surgical instruments, is an important and challenging research direction. This work reports the preparation of antibacterial surfaces via the electrodeposition of a conformal hydrogel of self‐assembling cationic peptide‐amphiphiles (PAs). Hydrogels of three PAs are electrodeposited: C16K2, C16K3, and C18K2, where Cn is an alkyl chain of n methylene groups and Km is an oligopeptide of m lysines. The processing variables (electrodeposition time, potential, pH, salt concentration, agitation) enable fine control of film thickness, demonstrating the flexibility of the method and allowing to unravel the mechanisms underlying electrodeposition. The electrochemically prepared hydrogels inhibit the growth of Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa in agar plates, and prevent the formation of biofilms of Acinetobacter baumannii and P. aeruginosa and the formation of A. baumannii colonies in solid media. C16K2 and C16K3 hydrogels outperform the antimicrobial activity of those of C18K2 while maintaining good compatibility with human cells.