The interest in assessing the presence of some chemical elements in seafood, such as halogens and sulfur, has been increasing. In this study, a novel analytical method was developed, enabling the determination of Br, Cl, F, I, and S in a single analysis in shellfish (brown-mussel, Perna perna), common octopus (Octopus vulgaris), and fish (argentine hake, Merluccius hubbsi), using ion chromatography coupled to mass spectrometry (IC-MS). It was observed that sample pre-treatment by oven-drying at 100 °C can cause F losses by volatilization, compared to other drying methods, such as oven-drying at 60 °C and freeze-drying. Also, the pH of the digests is not the only factor affecting halogen stabilization after microwave-induced combustion (MIC), and other aspects must be considered, such as the concentration of the analytes and the absorbing solution composition. MIC provided suitable recoveries (92% to 108%) for all analytes using 250 mmol L-1 NH4OH as the absorbing solution when combined with IC-MS determination. The trueness of the proposed method was also evaluated by analyzing standard reference materials (SRMs NIST 1566a and 2976, oyster and mussel tissues). Results did not present statistical differences (Student’s t-test, confidence level of 95%) compared to the certified/reference values (agreements varying from 95% to 109% for all analytes). Analyte content (mass fraction) varied in a large range: 7 to 181 mg kg−1 for Br; 1,285 to 24,176 mg kg−1 for Cl; 5 to 34 mg kg−1 for F; < 3.3 to 7 mg kg−1 for I; and 7,917 to 17,409 mg kg−1 for S. The proposed method is a novel and reliable analytical tool and, at the same time, new insights on the influence of solution pH and drying method on the sample preparation step were provided.