The microbiome consists of bacteria, yeasts, protozoa and viruses that live in symbiosis with the human body. Dysbiosis, or change in the microbiome, disrupts the balance with the immune system, triggers inflammation and contributes to connective tissue diseases (CTD). Interstitial lung diseases (ILDs) are disorders characterized by fibrosis of lung tissue and impaired lung function, and are a major cause of morbidity and mortality in patients with CTD. The gut-lung axis is established, but it is unclear whether gut dysbiosis contributes to ILD. Changes in the lung microbiome and high microbial burden are associated with worse prognosis and acute exacerbations in patients with CTD-ILD, especially in rheumatoid arthritis, systemic sclerosis, and dermatomyositis. Probiotics, as active microorganisms normalizing the intestinal flora, are proposed as a possible supportive treatment of CTD-ILD. Current knowledge about dysbiosis and CTD-ILD is incomplete, requiring further studies. The review focuses on clinical pulmonary aspects and therapeutic options.