On-surface synthesis has recently emerged as an effective route towards the atomically precise fabrication of graphene nanoribbons (GNRs) of controlled topologies and widths. However, whether and to what degree structural disorder occurs in the resulting samples is a crucial issue for prospective applications that remains to be explored. Here, we experimentally visualize ubiquitous missing benzene rings at the edges of 9-atom wide armchair nanoribbons that form upon cleavage of phenyl groups in the precursor molecules. These defects are referred to as ‘bite’ defects. 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 GNRs and assesses their effect on the performance of carbon-based nanoelectronic devices.