Inadequate choline intake-induced choline metabolic stress (CMS) has been divergently linked to metabolic dysfunction-associated steatotic liver disease (MASLD), yet underlying mechanisms remain unclear. We hypothesized that CMS modifies plasma-free amino acid (PFAA) signatures to influence MASLD risk. In a nested case–control study of 125 participants, dietary choline intake and blood choline metabolites were assessed together with targeted metabolomics and transcriptomic profiling. MASLD was characterized by low choline intake, reduced plasma betaine/choline ratio (Pbcr), elevated homocysteine, increased branched-chain amino acids (BCAAs), and depleted serine/glycine, achieving strong predictive accuracy (AUC = 0.90). CMS was associated with reduced lymphocytic transcripts involved in BCAA catabolism and altered mTORC1/Akt/IRS1 signaling. Nonlinear Pbcr- and intake-dependent MASLD risk patterns were attenuated after adjustment for genetic–metabolite networks. These findings identify CMS-responsive metabolic mediators supporting precision choline interventions.