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Enterotoxigenic <i>Escherichia coli</i> (ETEC) is closely associated with diarrhoea in children in resource-limited countries. This study aims to investigate the change of the mucosal microbiome and protein expression in the ileum induced by <i>E. coli</i> K88 (ETEC) using pigs as a model. Seven weaned male pigs were orally given ETEC (1 × 10⁹ CFU, <i>n</i> = 7), and the other seven received saline (CON, <i>n</i> = 7). Ileal tissues were obtained 48 hours after the ETEC challenge for both proteomic and mucosal microbiome analyses. Nine proteins were found with altered abundance between the two groups, including a decrease in FABP1 and FABP6, involved in bile acid circulation. The TLR-9 mediated pathway was also affected showing increased transcription of genes SIGIRR and MyD88. Correlations between the ileal proteins and mucosal bacterial taxa found included a positive correlation between Lactobacilllus and PPP3CA (r = 0.9, <i>p</i> < 0.001) and a negative correlation between Prevotella with CTNND1 (r = −0.7, <i>p</i> < 0.01). In conclusion, ETEC infection caused inflammation and impaired the circulation of bile acids and the mucosal microbiome may affect the expression of intestinal proteins. Further studies are needed to explain the exact roles of these affected processes in the pathogenesis of ETEC-triggered diarrhoea.