We have previously generated epidermal factor expressing Lactococcus lactis (EGF-LL) using a bioengineering approach, and shown that EGF-LL fermentation supernatant enhanced newly weaned pigs growth. The objective of the current study was to further understand the mechanisms behind this improved performance. Sixty-four piglets were weaned at 3 weeks of age and then fed ad libitum according to a 2-phase feeding program. Four pens with 8 pigs per pen were assigned to each of two treatments for 3 weeks: (1) EGF containing supernatant from EGF-LL culture (SuperEGF) or (2) blank M17GE media (Control). Consistent with previous findings, SuperEGF pigs had an increased average daily gain during week 3 post-weaning (433.4±10.86 vs 388.7±7.76g; P<0.05) and overall gain:feed ratio (0.757±0.03 vs 0.677±0.01kg/kg, P<0.05). Moreover, jejunal structure development was enhanced, and inflammation index was minimized in SuperEGF pigs as indicated by increased villi height (P<0.05), decreased lamina propria width (P<0.05), and higher expression of anti-inflammatory cytokine, IL-13 (P<0.05). Further, goblet cell numbers and Muc2 levels were increased in SuperEGF pigs. Interestingly, the weaning-induced decrease of glucose cotransporter sodium-glucose linked transporter 1 (SGLT1) and glucagon-like peptide-2 (GLP2) levels was reversed by SuperEGF supplementation. Our findings add to our understanding of the mechanisms behind enhancing piglet performance by EGF containing fermentation product.