This study investigated the effect of preserving wheat and barley grains with an organic acid liquid surfactant mould inhibitor compared to conventional artificial drying and assessed its effects on the health and performance of pigs post-weaning (PW). A 2 × 2 factorial arrangement was conducted to investigate the interaction between grain preservation method (dried vs. preserved) and zinc oxide (ZnO) inclusion (yes vs. no) on growth performance, diarrhoea scores and incidence, and total tract nutrient digestibility. One hundred and ninety-two pigs (3 pigs/pen; 16 replicates/treatment) were assigned to one of four experimental diets for 35 days: (1) dried grain diet, (2) preserved grain diet, (3) dried grain diet with ZnO and (4) preserved grain diet with ZnO. Diets were formulated to contain similar levels of net energy and standardised ileal digestible lysine. On day 35 PW, 24 pigs (12 replicates/treatment) from the non-ZnO supplemented groups were euthanised and digesta was collected for coefficient of apparent ileal digestibility (CAID), gut microbial population and volatile fatty acid analysis. Stomach tissue was also collected for gene expression analysis, as well as small intestine samples for gut morphology. Notable improvements in grain quality were observed in the preserved grain, including a reduction in grain pH, mould presence, and contamination by mycotoxins, specifically deoxynivalenol in wheat and barley, and ochratoxin A and HT-2 toxin in barley. The preserved grain diet improved average daily gain (ADG; P < 0.01) and body weight (BW; P < 0.01) compared to the dried grain diet. The incorporation of ZnO increased average daily feed intake (ADFI; P < 0.01) and BW (P < 0.05) in the dried grain diet, however, ZnO did not affect ADFI (P > 0.05), and reduced ADG and BW in the preserved grain diet (P < 0.05). Pigs offered the preserved grain diet had reduced faecal scores and diarrhoea incidence compared to those offered the dried grain diet (P < 0.05). Supplementation of ZnO reduced faecal scores and diarrhoea incidence compared to non-supplemented pigs (P < 0.001). On day 35 PW, the preserved grain diet had improved CAID of nitrogen and gross energy (P < 0.05), lower levels of colonic branched-chain volatile fatty acids (P < 0.05), and beneficial shifts in gut microbial populations. Specifically, there was a reduction in ileal Streptococcus (P < 0.001) and an increased abundance of colonic Faecalibacterium (P < 0.05). In conclusion, organic acid preservation improved grain quality, benefiting post-weaned pigs through improved nutrient digestibility and gut health, thus enhancing overall growth performance PW.