Developing a successful protocol for banana in vitro culture is a guarantee for the mass propagation of pathogen-free, high-quality, true-to-type planting materials with low production costs. The current work aimed to investigate the influence of increasing copper levels in an MS medium on endophytic bacterial contamination; shoot multiplication; rooting and the acclimatization of in vitro cultured banana; minerals and chlorophyll content; antioxidant enzymes activity; electrolyte leakage; and the genetic stability of banana regenerants. Four different concentrations of copper sulphate (0.025 as a control, and 30, 60, and 120 mg L−1) were examined. The growth of the endophytic bacteria was inhibited at 60 mg L−1 of copper sulphate which recorded zero contamination, without a significant difference at 120 mg L−1. However, 0.025 mg L−1 of copper sulphate was optimal for the maximum shoot number and shoot length (10 shoots and 6 cm, respectively) without significant differences at 30 mg L−1. The root length of banana plantlets was significantly enhanced at 30 mg L−1 of copper sulphate but without significant differences to the control, regarding the number of roots (9.92 cm and 3.80 roots, respectively). In vitro plants were acclimatized successfully at 30 mg L−1 of copper sulphate with 100% survival. The uptake of minerals, antioxidant enzyme activity and electrolyte leakage was improved because of the copper sulphate, but the chlorophyll level decreased. RAPD profiling showed polymorphism in only one plant treated with 60 mg L−1 of copper sulphate, with an average of 1.8%. The genome template stability percentage was almost 100% for all treated plants.