The complete dissolution of silicate-containing materials, often necessary for elemental determination, is generally performed by microwave-assisted digestion involving the forced use of hydrofluoric acid (HF). Although highly efficient in dissolving silicates, this acid exhibits many detrimental effects (e.g., formation of precipitates, corrosiveness to glassware) that make its removal after digestion essential. The displacement of HF is normally achieved by evaporation in open-vessel systems: atmospheric contamination or loss of analytes can occur when fuming-off HF owing to the non-ultraclean conditions necessarily adopted for safety reasons. This aspect strongly hinders determination at the ultra-trace level. To overcome this issue, we propose a clean and safe microwave-assisted procedure to induce the evaporative migration of HF inside a sealed “vessel-inside-vessel” system: up to 99.9% of HF can be removed by performing two additional microwave cycles after sample dissolution. HF migrates from the digestion solution to a scavenger (ultrapure H2O) via a simple physical mechanism, and then, it can be safely dismissed/recycled. The procedure was validated by a soil reference material (NIST 2710), and no external or cross-contamination was observed for the 27 trace elements studied. The results demonstrate the suitability of this protocol for ultra-trace analysis when the utilization of HF is mandatory.