Mild cognitive impairment (MCI) refers to cognitive alterations with preservation of functionality. Individuals with this diagnosis have a higher risk of developing dementia. Non-pharmacological interventions, such as physical exercise, are beneficial for the cognition of this population. However, the impact of resistance training (RT) on the brain anatomy of older adults with MCI has not yet been clarified. This study aimed to investigate the effects of RT on cognition and brain anatomy in MCI. Forty-four older adults with MCI, 22 in the training group and 22 in the control group, were evaluated in neuropsychological tests and magnetic resonance imaging at the beginning and end of the study, which lasted 24 weeks. We used repeated measures ANOVA. The training group showed better performance in verbal episodic memory after intervention. The control group showed a decrease in gray matter volume in the hippocampus and precuneus, while the training group showed no reduction in the right hippocampus and precuneus. However, it showed a decrease in the volume of these regions on the left side and in the left superior frontal gyrus. In the analysis of white matter integrity, fractional anisotropy increased in the training group and decreased in the control group. Axial diffusivity decreased in the training group, while radial diffusivity increased in the control group, and mean diffusivity varied according to the tract evaluated. RT improves memory performance, positively influences white matter integrity parameters, and plays a protective role against atrophy of the hippocampus and precuneus in MCI.