Frailty is a geriatric syndrome causing a reduction in the body’s functional reserves. Proper nutrition may be helpful in delaying transitioning older adults from pre-frail to frailty syndrome. The present study evaluates the nutritional status of pre-frail patients who underwent nutritional intervention and metabolomic changes resulting from this intervention. Sixteen pre-frail patients (68.4 ± 5.5 years old; 81.3% women) were enrolled for nutritional intervention, and twenty-nine robust elderly people (69.3 ± 5.3 years old; 82.8% women) were the control group. Pre-frail patients consumed 1.0 g protein/kg BW/day for eight weeks through diet modification and an additional daily intake of a protein powder formula. Taken measurements included: Nutritional anthropometry, assessment of food intake, and blood serum analysis with an untargeted metabolomic assessment. Protein consumption increased by 25.8%; moreover, significant increases in body weight (+1.2 kg; p = 0.023) and muscle mass index (+0.1 kg/m2; p = 0.042) were also observed. The untargeted metabolomic assay showed a significant increase in arachidonic acid (p = 0.038), and valine (p = 0.008) among pre-frail patients. Increased protein consumption is reflected in improved anthropometric and biochemical parameters of pre-frail patients. Moreover, metabolomic assay can be a useful tool in determining compliance with dietary recommendations.