Rheumatic diseases as well as inflammatory bowel disease (IBD) have been associated with the occurrence of non-cystic fibrosis bronchiectasis (NCFB). There are few data on NCFB and adverse events from immunosuppressive or biological response modifier therapy in patients with rheumatoid arthritis (RA) or IBD and NCFB. We identified 37 patients with NCFB and rheumatic disease, and nine patients with inflammatory bowel disease that received immunomodulatory treatment. We retrospectively analysed adverse pulmonary events. In nine patients with RA, the association between disease activity score (DAS) and spirometry was analysed in a small cohort study. Pulmonary side effects occurred in 50% of patients, most commonly respiratory infections, and resulted in a change of immunomodulatory treatment in 37% of patients. Spirometry and exacerbation rate was not different in NCFB patients with RA or IBD as compared with NFCB due to other causes. The incidence of pulmonary adverse events was highest in patients treated with conventional immunomodulatory treatment, especially methotrexate, as compared with patients with NCFB treated with newer biological therapies. Three patients were started on azithromycin because of recurrent bronchitis and had no events afterwards. Serial assessment of DAS and spirometry showed that a rise in DAS was associated with lung function decline and vice versa. Currently used immunosuppressive drugs can be used in NCFB albeit under close follow-up. The role of azithromycin for infection prevention needs further research. An association between DAS and lung function was shown.