Background: Point-of-care testing (POCT) devices offer a rapid alternative for lipid assessment, but comprehensive analytical validation against reference laboratory methods remains limited. Objective: This study aimed to evaluate the agreement, systematic bias, and diagnostic performance of the Mission^® Cholesterol 3-in-1 system for lipid profile measurements and atherogenic ratios. Methods: A prospective cross-sectional agreement study was conducted among 120 participants. Lipid profiles were measured using eleven Mission^® Cholesterol 3-in-1 analyzers and compared with those measured using the reference laboratory method. Agreement was assessed using the intraclass correlation coefficient (ICC), concordance correlation coefficient (CCC), coefficient of determination ($R^2$), root mean square error (RMSE), mean absolute error (MAE), percentage bias, Bland–Altman plots, Passing–Bablok regression, and diagnostic accuracy. Results: Triglycerides demonstrated excellent agreement (ICC = CCC = 0.972; bias = 5.19%), whereas total cholesterol, HDL-C, non-HDL-C, and LDL-C showed good agreement (ICC range: 0.817–0.854). Among the atherogenic ratios, TG/HDL-C (ICC = 0.932) and TG/LDL-C (ICC = 0.931) exhibited the highest concordance. Passing–Bablok regression revealed constant bias for all analytes, except for LDL-C estimated using the Sampson equation and the TG/LDL-C ratio, while proportional bias was observed for all analytes, except for triglycerides and the TG/LDL-C ratio. Despite these systematic differences, diagnostic performance remained excellent, with sensitivities of 94.29–98.33% and specificities of 68.33–91.80%. Conclusion: The Mission^® Cholesterol 3-in-1 system shows good analytical agreement with laboratory testing, particularly for triglycerides and the HDL-C, TG/HDL-C, and TG/LDL-C ratios. Although systematic bias limits complete interchangeability with reference methods, its excellent diagnostic performance supports its use as a rapid point-of-care screening tool, especially in resource-limited settings.