The use of medicinal zinc oxide (ZnO) to prevent diarrhoea post-weaning will be banned in the EU from 2022. Therefore, new alternatives are needed to avoid an increase in diarrhoea and higher antibiotic use. A low dietary CP level has shown to lower the frequency of diarrhoea in pigs, due to lower microbial protein fermentation in the colon as well as improved conditions in the small intestine after weaning. The objective of this study was to examine the effect of decreased CP levels post-weaning as an alternative to medicinal ZnO on gut morphology and histopathology. Five hundred and sixty pigs were randomly assigned into one of six groups receiving a two-phase diet from 5.5 to 15 kg: positive control group (PC) with medicinal ZnO and standard levels of protein (19.1–18.4% CP), negative control group (NC) without medicinal ZnO and standard levels of protein (19.1–18.4% CP). The remaining four low protein groups were a low-standard (LS) CP level (16.6–18.4% CP), a low-low (LL) CP level (16.6–16.2% CP), a very low-high (VLH) CP level (14–19.3% CP) and a very low-medium (VLM) CP level (14–17.4% CP). Individual BW was recorded at day 0, 10 and 24 post-weaning, and all antibiotic treatments were recorded. Tissue samples from the small intestine (mid-jejunum) for morphological and histopathologic analysis, organ weights, blood and urine samples were collected at day 10 and 24 post-weaning from a total of 90 sacrificed weaners. The results demonstrated no differences in intestinal morphology between groups, but the histopathology showed a damaged brush border score in VLM and VLH pigs . In addition, a lower blood urea nitrogen in VLM pigs at 24 days was found. The LL and VLM pigs had a significantly decreased average daily gain in the overall trial period compared to PC and NC pigs. Conclusively, intestinal brush border was damaged by the very low protein diet at 24 days post-weaning, but intestinal morphology was unaffected by dietary strategy.