Housing of pigs in barren, stimulus-poor housing conditions may influence their immune status, including antibody responses to (auto-)antigens, and thus affect immune protection, which will influence the onset and outcome of infection. In the present study, we investigated the effects of environmental enrichment versus barren housing on the level of natural (auto-)antibodies (NA(A)b) and their isotypes (IgM and IgG) binding keyhole limpet hemocyanin (KLH), myelin basic protein (MBP), and phosphorycholine conjugated to bovine serum albumin (PC-BSA) in pigs co-infected with porcine reproductive and respiratory syndrome virus (PRRSV) and Actinobacillus pleuropneumoniae (A. pleuropneumoniae). Pigs (n = 56) were housed in either barren or enriched pens from birth to 54 days of age. They were infected with PRRSV on 44 days of age, and with A. pleuropneumoniae 8 days later. Blood samples were taken on 7 different sampling days. Housing significantly affected the overall serum levels of NA(A)b binding KLH, MBP and PC-BSA, and before infection barren housed pigs had significantly higher levels of NA(A)b than enriched housed pigs, except for KLH-IgM and PC-BSA-IgG. Infection only affected the IgM, but not the IgG isotype. Moreover, changes in MBP-IgM and PC-BSA-IgM following infection were different for enriched and barren housed pigs. These results suggest that the effect of infection on NA(A)b is influenced by housing conditions and that NA(A)b, especially IgM may be affected by infection.