Weaning of piglets is associated with important changes in gut structure and function resulting from stressful events such as separation from the sow, moving to a new facility and dietary transition from a liquid to a solid feed. This may result in post-weaning diarrhoea and a decrease in feed intake and growth. In humans, the cyanobacterium Spirulina platensis (SP) and the freshwater microalga Chlorella vulgaris (CV) are known for their beneficial health effects. This study aimed to determine the effects of early oral administration of Spirulina and Chlorella in piglets on mucosal architecture and cytokine expression in the intestine around weaning, and consequences on growth performance and diarrhoea incidence. The experiment was conducted on 108 suckling piglets of 14 days of age (initial BW = 4.9 +/- 0.7 kg) and weaned at 28 days of age (day 0). Animals received orally 385 mg/kg BW per day of SP or CV, or water (negative control (NC)) during 4 weeks from day -14 to day 14 and their growth performance was measured daily. After weaning, growth, feed intake and diarrhoea incidence were measured daily. Intestinal morphology and functionality were assessed at day -1, day 2, and day 14. During the suckling period, average daily gain (ADG) in SP piglets was higher, resulting in a higher weaning BW compared to NC and CV piglets (P < 0.05). No significant difference between treatments was observed for ADG, average daily feed intake, and gain to feed (G: F) ratio after weaning, but the extent of growth retardation after weaning was the lowest in piglets supplemented with Chlorella (P < 0.01). Supplementation with Spirulina reduced diarrhoea incidence by 50% from day 0 to day 14 (P < 0.05). Mucosal architecture at the jejunum was unaffected by Spirulina or Chlorella administration (P > 0.10). Shorter ileal villi were measured in SP and CV piglets than in NC piglets (P < 0.05). Cytokine expression did not differ between treatments in response to weaning. At day 14, IL-8 expression in the ileum was higher in SP piglets, while IL-1 beta expression in the jejunum was higher in CV piglets (P < 0.05). This study shows that Spirulina administration around weaning alleviates diarrhoea in weaned piglets, without marked modulation of local inflammation.