Osteoarthritis (OA) is a degenerative joint disease that affects humans and animals worldwide. Its early diagnosis remains challenging due to subtle clinical signs and late radiographic changes. This study aimed to explore candidate biomarkers associated with spontaneous OA and to investigate their correlation with ultrasonographic scores to support early diagnosis. Clinical, radiographic, and ultrasonographic evaluations were performed on 52 equine metacarpophalangeal joints, with and without OA, allowing joint scoring and classification into osteoarthritis (OAG) and control groups. Synovial fluid samples were analyzed for cartilage degradation (C2C), untargeted ¹H NMR-based metabolomics, and lipid peroxidation (TBARS). Statistical analyses included Student’s t-test, Mann–Whitney U test, univariate and multivariate metabolomic analyses, and Spearman’s correlation (p < 0.05). Ultrasonography revealed higher scores in the synovial fold, membrane, and fluid, indicating synovitis as the predominant finding in the acute phase. C2C and TBARS concentrations were significantly higher in the OAG. Seven metabolites differed between groups, with citrate and TBARS showing the strongest correlations with ultrasonographic scores. These findings suggest increased metabolic activity and lipid peroxidation in early OA and highlight citrate and TBARS as potential auxiliary biomarkers for early diagnosis associated with synovitis.