Physical exercise has been established as an intervention in the integral approach for the physical, functional, and social health of older adults. The objective of this study was to determine the effects of a high-intensity functional training (HIFT) program on the physical condition and functional capacity of an elderly Colombian population with mild cognitive impairment. This research corresponds to a blind randomized controlled clinical trial. A total of 169 men and women aged over 65 years were evaluated and distributed in two groups: the experimental group that received a 12-week HIFT intervention (n = 82) and the control group (n = 87) that received general recommendations on the benefits of physical exercise. The outcome variables included physical condition, assessed using the Senior Fitness battery (SNB); Fried's frailty phenotype was applied, and gait and balance were assessed using the Tinetti scale. For the functional variables, activities of daily living, instrumental activities of daily living, and advanced activities of daily living were evaluated. All variables were measured pre- and post-intervention. Statistically significant improvements were observed in the IG for gait stability and balance (p < 0.001), as well as for independence in activities of daily living (p = 0.003), and instrumental and advanced activities (p < 0.001). Likewise, greater functionality was found when assessed with the SNB (p < 0.001), except for upper limb strength. The frailty classification did not show changes post-intervention (p = 0.170) nor in the group x time interaction. MANCOVA analysis showed that regardless of gender, health level, age, BMI, cognition, and health level, the HIFT intervention produced better results in functional capacity, balance, and gait (F = 0.173, p < 0.001, Wilks' λ = 88.231).