The group of nontuberculous mycobacteria (NTM) includes about 200 mycobacteria that are widespread in the natural environment as free-living saprophytic bacteria, commensals or symbionts. NTM, also referred to as atypical mycobacteria, are mostly apathogenic; nowadays, they are increasingly important environmental opportunistic pathogens. This study continues the work of previous studies which investigated the individual and synergistic effect of different essential oils (EOs) on NTM. The aim was to investigate the effect of the interaction of the common juniper (Juniperus communis) EO and the antimicrobials, amikacin, clarithromycin and rifampicin, against Mycobacterium avium and M. intracellulare using the checkerboard synergy method in an enriched Middlebrook 7H9 broth. Morphological changes of treated NTM cells were observed with a transmission electron microscope. The most synergistic combinations were found at subinhibitory concentrations of the common juniper EO and rifampicin against both tested NTM and this EO and clarithromycin against M. avium. A slightly smaller number of synergistic effects on both NTM were found using a combination of this EO and amikacin. Combinations of clarithromycin and the common juniper EO showed no synergism against M. intracellulare. The exposure of both NTM to synergistic combinations of this EO and antimicrobials caused significant morphological changes in mycobacterial cells. Synergism with the combined use of EOs and antimicrobials allows the use of low effective concentrations via the sustained antimicrobial effect of the tested substances, but with potentially reduced toxicity.