Type 2 diabetes mellitus (T2DM) is a leading cause of disability globally. Frailty is a high-impact geriatric condition that increases the risk of negative health outcomes and imposes remarkable health and social burden. Both frailty and T2DM show multifaceted pathophysiology, phenotypic heterogeneity, and fluctuating manifestations that challenge their management, especially when the two conditions co-occur. Muscle wasting and its correlates (e.g., metabolic perturbations and functional decline) that underlie frailty may exacerbates clinical manifestations of T2DM in older people, resulting in worse prognosis. The intrinsic complexity of frailty and T2DM has hampered the identification of clinically meaningful biomarkers to track the clinical progression of the two conditions over time and to monitor the efficacy of pharmacological and lifestyle interventions. Here, we propose an innovative approach for biomarker identification that couples multi-platform analytical determinations with chemometric modeling strategies. This novel multi-marker discovery process is described in the context of the "Metabolic biomarkers of frailty in older people with type 2 diabetes mellitus" (MetaboFrail) study that aimed at identifying metabolic biomarkers of frailty in functionally limited older persons with T2DM.