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Background The prevalence of infection with non-tuberculous mycobacteria (NTM) has been increasing in people with cystic fibrosis (pwCF) over the past 30 years. Emerging reports of beneficial effects of CFTR modulators, particularly elexacaftor/tezacaftor/ivacaftor (ETI), on the rates of NTM acquisition and persistence are encouraging. In this observational study, we evaluate the impact of the introduction of ETI on the prevalence of NTM infection within a cohort of pwCF living in sub-tropical Queensland, Australia.Methods We examined the impact of ETI introduction on rates of NTM isolation in pwCF attending an adult CF centre and two large regional clinics providing CF care. Data on NTM infection were collected for a minimum of 2 years pre- and post-initiation of ETI.Results In total, 271 (84.2%) were commenced on ETI with 33 (12.2%) of these pwCF isolating an NTM species on one or more occasion. The number of pwCF isolating Mycobacterium abscessus (Mabs) remained static across the 4-year period of analysis. However, there was a trend towards declining numbers of pwCF isolating either Mycobacterium intracellulare or other NTM species across the surveillance period.Conclusions ETI therapy was not associated with reduced rates of NTM isolation from sputum over the first 2 years of treatment. However, at a species level, two distinct patterns of change were seen with a trend towards a reduction in the isolation of M. intracellulare, while the rates of Mabs isolation remained unchanged. The reasons for this remain unclear at present but highlight the need for ongoing vigilance with screening for NTM in the setting of ETI therapy.