Diphenylalanine (Phe2) is the primary building block of many self-assembling nanostructures that are important in biology and materials science. Understanding the detailed mechanism of their formation requires knowledge of the structural motives that the smallest oligomers attain at the very first steps of the process. Herein, we first employed high-resolution mass spectrometry to assign protonated Phe2 and its 2–13-unit oligomers formed in the gas phase from solution via electrospray ionization and then used cold ion spectroscopy to record UV and IR spectra for the monomer, dimer and hexamer. UV spectroscopy suggests the likely lack of specific strong proton–p interactions in oligomers larger than octamers, implying their certain structural stabilization. IR spectroscopy and quantum chemical calculations, enhanced by neural network-based conformational search, jointly determined the lowest-energy structures of the Phe2 monomer and dimer.