Urbanisation is associated with air and soil pollution, particularly from heavy metals. One of the tissues most exposed to such pollutants is the midgut epithelium as insects may ingest these pollutants with food. Bees are one of the most important urban insects, providing important ecosystem services such as pollination. However, to the best of our knowledge, no studies have investigated the possible histological alterations to the midgut epithelium of bees caused by urbanisation. We sampled workers of the ground-nesting, primitively eusocial bee Halictus scabiosae in a large metropolis (Milan), with the aim to test if individuals from areas characterised by higher urbanisation and consequently higher pollution levels—defined here by a greater proportion of roads—exhibit greater histological tissue and cellular alterations in the midgut epithelium. We obtained semi-thin sections of the midgut through histological techniques, and then adopted a semi-quantitative approach to assess morphological damage. The midgut presented a range of histological alterations including epithelium disorganisation, vacuolisation, and nucleus karyorrhexis (one of the stages of cellular death). We found higher histological damage score (calculated taking into account all found alterations) and frequency of karyorrhectic nuclei in sites with a higher proportion of roads (i.e. more urbanised). The observed alterations may underline a potential impairment of the digestive function in highly urbanised areas.