Nanoscale energy harvester holds promise for the development of self-powered nanosystems, while molecular self-assembly of bio-inspired materials has attracted much research effort in recent years due to its potential to fabricate novel bottom-up structures for new applications. Among them diphenylalanine (FF) peptide has been widely explored recently. Strong piezoelectricity was demonstrated in FF peptide nanotubes. Here we report a new and scalable approach to the controlled fabrication on various substrates of vertically aligned FF peptide microrods with uniform polarization. Piezoelectric FF peptide microstructures were fabricated on various substrates through a novel epitaxial growth approach. We start by engineering a textured seed layer with preferential vertical orientation, and then grow the FF peptide microrods epitaxially from this seed layer. The low-temperature process produced vertically aligned FF peptide microrods with hexagonally arranged nanochannels and uniform polarization. Direct measurement of the piezoelectricity was achieved for the first time from a solid FF peptide single crystal and yielded an effective piezoelectric coefficient d₃₃ at 9.9 pm/V. Our work can enable new applications of bio-inspired materials in areas such as energy harvesting and storage, electromechanical sensing and actuation, drug delivery, as well as fundamental studies of FF-based structures.