Background and Objectives: This study investigated whether capillary and intravenous sampling affect acylcarnitine and amino acid profile results analyzed by tandem mass spectrometry. Methods: The study included 120 patients either diagnosed with an inherited metabolic disease or undergoing evaluation for a suspected metabolic disorder at the Department of Pediatric Nutrition and Metabolism, Selçuk University Faculty of Medicine. Paired capillary and intravenous blood samples were collected simultaneously, applied to filter paper, and analyzed by LC-MS/MS to determine acylcarnitine and amino acid profiles. Results: Significant differences were observed between capillary and intravenous samples for several acylcarnitines, including C0, C2, C8, C8.1, C10, C10.1, C14.1, C16, and C18.1 (p < 0.05). In the amino acid profile, arginine, aspartic acid, citrulline, glutamic acid, glycine, leucine + isoleucine, methionine, tyrosine, and the methionine/phenylalanine ratio differed significantly between sampling methods (p < 0.05). Despite these differences, Cohen’s kappa analysis showed high agreement between capillary and venous samples for most parameters (78.3–100%) when categorized as low, normal, or high based on reference ranges. Additionally, no significant discrepancies were found in key diagnostic parameters among patients with specific inherited metabolic diseases. Conclusions: Although certain acylcarnitine and amino acid levels differed between capillary and intravenous samples, overall diagnostic agreement was high. However, since the study group did not include any patients with fatty acid oxidation disorders, a separate confirmatory study is needed for this condition. Larger multicenter studies involving more patients and a wider range of metabolic disorders are needed to better understand the clinical impact of sampling method on dried blood spot analyses.