The use of organic acids in diets for livestock animals is interest due to their being potentially beneficial in maintaining gut homeostasis and controlling pathogenic bacterial growth. The objective of this study was to evaluate the influence of two doses of formic acid supplementation for six weeks to weaner pigs. The long-term effects of formic acid were tested for growth performance, microbiota composition in the jejunum using 163 rRNA, expression of marker genes of inflammation in the jejunum, and quantification of acid-secreting cells in the gastric oxyntic mucosa using immunohistochemistry. Three diets containing no (control; CO), 1.4 g/kg (low formic acid; LFA) or 6.4 g/kg (high formic acid; HFA) free formic acid were fed to 36 pigs for 42 d from 7 d post-weaning (7.1 +/- 1.0 kg live weight) until the end of the trial (27.7 +/- 5.5 kg live weight); they were housed in individual cages for six weeks. During the first three weeks, formic acid supplementation, at any of the dosage above, increased average daily gain (ADG) (P = 0.004), tended to increase average daily feed intake (ADFI) (P = 0.08) and tended to decrease g of feed to g of gain (F:G) (P = 0.08) while no effect was observed during the last three weeks. At the end of the trial, formic acid supplementation had only a minor effect on the microbiota composition in the jejunum. A higher microbiota diversity (Chaol index P < 0.05) was found in the HFA group than in the CO group. The Control group showed a higher abundance (P < 0.05) of Gemella, Lactobacillus and Parvimimoas than the HFA and LFA groups, higher levels of Acinetobacter, Fusobactrium, Leuconostoc respect to the HFA group and of Turcibacter as compared to the LFA group. The abundance of Streptococcus was lower in the CO group than in the HFA group and higher than in the LFA group. The jejunal expression of C-C Motif Chemokine Ligand 2 (CCL20) was higher in the HFA group respect to the LFA group. Formic acid intake did not affect the thickness of the gastric mucosa, the number of parietal cells and stomach weight. This study showed that the addition of formic acid to piglet diets improved growth performance during the first period after weaning and that the long-term supplementation of formic slightly affected the microbiota composition according to the dose.