The goal was to analyze the effect of two different training programs on functional autonomy, balance, and body composition in aged women and to determine the influence of their cognitive function. Older women aged between 60 to 80 years old were invited to participate in the study. A block randomisation method was used to allocate participants to the Pilates group (PEP), the Muscular group (MEP) and the control group (CG) with equal sample sizes (n = 20). PEP or MEP were required to train twice a week (1 hour/session) in a moderate to vigorous intensity for 18 weeks. Functional autonomy was assessed with the GDLAM protocol. The cognitive function, withthe Mini-Mental State (MMS). Static balance, with a force platform (Kistler 9286AA). Body composition, with a dual-energy X-ray bone densitometry. Research staff performing the assessment and statistical analysis was blinded. Eighty participants were randomized, 16 women did not meet the inclusion criteria and 4 refused to participate. 60 participants were analysed. Either Pilates or Muscular group improved significantly (P ≤ 0.05) in every GDLAM test. Pilates had a better general functional condition index (IG) than the Muscular group (P = 0.042). There was a significant interaction (P ≤ 0.05) between the cognitive function and two items of the GDLAM test. The amplitude of displacement of the center of pressure in the antero-posterior plane decreased significantly in the Muscular group (P = 0.04). The total lean body increased in the Pilates (P =< .001) and the Muscular groups (P = 0.05). Pilates should be recommended for improving the general functional condition of older women, while the Muscular exercise is effective for enhancing the static balance. Both exercise programs are effective for increasing the total lean body. The cognitive function interacts with some functional autonomy parameters Trial registration: ClinicalTrials.gov (identifier: NCT02506491; available from https://clinicaltrials.gov/show/NCT02506491). •Pilates resulted in a greater increase in the general functional condition of older women than muscular exercise program.•Better cognitive function led to better agility pattern as well as to a better general functional condition.•Pilates and muscular exercise programs led to significant increase in lean body mass.•Muscular exercise program improved the two-leg static balance.