Abstract This study investigated the effect of feeding Cyberlindnera jadinii yeast on the development of gastrointestinal function and health in piglets during the first two challenging weeks after weaning. Changes in gastrointestinal function were mainly attributed to weaning, and not to dietary treatment. The post-weaning (PW) transcriptome profiles differed between dietary treatments showing an overall higher number of differentially expressed genes (DEGs) in control piglets than in yeast-fed piglets. DEGs in jejunum and ileum were compared between sampling timepoints within each feeding group and divided into clusters with similar expression trends. Pathway enrichment analysis was run on each cluster to reveal PW physiological changes. Weaning induced downregulation of several immune functions in the control piglets, which was not as evident in the yeast fed piglets. The results indicate that feeding C. jadinii yeast can improve PW gut homeostasis and give more robust piglets.