Influenza A virus (IAV) infection is a recognized cause of acute respiratory disease in pigs that can culminate in the decline of performance due to increasing feed conversion and costs of antimicrobial drugs to control secondary infections. Biosecurity practices are the key to prevent transmission of highly contagious agents. The aim of this study was to assess the effect of biosecurity practices on IAV seroprevalence through a cross-sectional study carried out in 404 sows from 21 herds. An indirect ELISA was used to detect antibodies against a nucleoprotein of IAV. To evaluate IAV subtypes (H1N1pdm09, H1N2 and H3N2), all samples positive by ELISA were tested using the hemagglutination inhibition assay (HI). Prevalence ratios (PR) estimates were calculated using multivariate Poisson regression accounted with survey weights. Sixty-four percent (261/404) of sows were positive in the rNP-ELISA and the estimated prevalence was 63.9% (95% CI 55%–73%). All farms had at least one seropositive sow; the frequency of IAV subtypes found in seropositive sows was 51.9% for H1N1pdm09, 38.1% for codetection H1N1pdm09 and H1N2, 8.6% for H1N2, and 0.6% for codetection H1N1pdm09 and H3N2, and 19 herds presented coinfection of H1N1 pdm09 and H1N2. Variables significantly associated with IAV seroprevalence found in the final model were ‘bird-proof net’ (PR = 0.75; 95% CI: 0.65–0.86) and ‘gilt acclimatization unit’ (PR = 0.57, 95% CI: 0.50–0.66), showing a protective effect against IAV seroprevalence, and ‘external replacement’, which had a positive effect on IAV seroprevalence (PR = 1.38, 95% CI: 1.17–1.64). This study suggests that preventing contact among wild species and swine and using an adaptation area for animals before entry into the herd can be strategies to control the influenza virus in breeding herds.