On-surface synthesis has recently emerged as an effective route towards the atomically precise fabrication of graphene nanoribbons of controlled topologies and widths. However, whether and to which degree structural disorder occurs in the resulting samples is a crucial issue for prospective applications that remains to be explored. Here, we experimentally identify missing benzene rings at the edges, which we name bite defects, as the most abundant type of disorder in armchair nanoribbons synthesized by the bottom-up approach. First, we address their density and spatial distribution on the basis of scanning tunnelling microscopy and find that they exhibit a strong tendency to aggregate. Next, we explore their effect on the quantum charge transport from first-principles calculations, revealing that such imperfections substantially disrupt the conduction properties at the band edges. Finally, we generalize our theoretical findings to wider nanoribbons in a systematic manner, hence establishing practical guidelines to minimize the detrimental role of such defects on the charge transport. Overall, our work portrays a detailed picture of bite defects in bottom-up armchair graphene nanoribbons and assesses their effect on the performance of carbon-based nanoelectronic devices.