Recent innovations in integrated microfluidic systems have advanced the frontier of personalized medicine by leveraging engineered aggregation phenomena to decode complex molecular behaviors. These developments enable the creation of microsystems that translate biological signals into actionable diagnostics tailored to individual health profiles. We present a handheld spinning platform with centrifugal microfluidics (HSP-CM)—a compact, electricity-free diagnostic microsystem designed for ultra-low-cost (~$1.40 USD) detection of urinary total protein (UTP), a key biomarker associated with disease-related protein aggregation. The HSP-CM integrates surface-engineered microchannels with tunable hydrophilic–hydrophobic properties, facilitating precise control over protein aggregation and reagent mixing during centrifugal activation. This personalised diagnostic tool provides rapid (~3 minutes), sensitive, and colourimetric quantification of UTP from minimal sample volumes (5 μL), achieving a detection limit of 3.49 μg/mL. Clinical validation across samples from healthy individuals and patients with myocardial infarction revealed a strong correlation (R = 0.9481) and agreement (90.32%) with conventional laboratory assays. By embedding aggregation science into a portable microsystem, HSP-CM exemplifies a new class of accessible, non-invasive diagnostics tailored for individualised health monitoring, particularly in resource-constrained environments.