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We sought to prospectively characterize the nutritional status of adults ≥ 19 years (n=22, 27% males) and children (n=38, 61% male) with genetically-confirmed primary mitochondrial disease (PMD) to guide development of precision nutritional support strategies to be tested in future clinical trials. We excluded subjects who were exclusively tube-fed. Daily caloric requirements were estimated using World Health Organization (WHO) equations to predict resting energy expenditure (REE) multiplied by an activity factor (AF) based on individual activity levels. We developed a Mitochondrial Disease Activity Factors (MOTIVATOR) score to encompass fatigue typical of PMD. PMD cohort daily diet intake was estimated to be 1,143 ± 104.1 Kcal in adults (mean ± SEM, 76.2% of WHO-MOTIVATOR predicted requirement), and 1,114 ± 62.3 Kcal in children (86.4% predicted). A total of 11/22 (54.5%) adults and 18/38 (47.4%) children with PMD consumed ≤75% predicted daily Kcal needs. Malnutrition was identified in 16/60 (26.7%) PMD subjects. Increased protein and fat intake correlated with improved muscle strength in those with insufficient daily Kcal intake (£75% predicted); higher protein and fat intake correlated with decreased muscle fatigue; and higher protein, fat and CHO intake correlated with improved quality of life (QoL). These data demonstrate the frequent occurrence of malnutrition in PMD and emphasize the critical need to devise nutritional interventions to optimize clinical outcomes.