Biomass is increasingly being used as an alternative energy source to fossil fuels. Of particular concern is that during combustion of biomass rich in silica (SiO2), such as sugarcane and many other grasses, the silica can convert into a crystalline form. Exposure to crystalline silica can potentially cause respiratory disease, such as silicosis. To improve understanding of the potential health risk, a robust and rapid method for quantifying the amount of silicon (Si) in plant material is required. Traditional methods do not usually account for Si in organic materials. This paper, therefore, proposes a new methodology based on a closed vessel microwave digestion using hydrofluoric acid (HF). To test the method, sugarcane leaves were digested and the solutions analysed by inductively coupled plasma atomic emission spectroscopy (ICP-AES), with an HF-resistant setup, and two external calibration standard sets in an HF-H3BO3-matrix and HNO3-matrix. The concentration of Si found in the reference materials was consistent with previously published values and Si loss during the sample preparation was minimal. The elemental recoveries from the reference materials were generally good (85–115% for Al, Ca, Cu, Fe, K, Mg, P, Si, Sr, Ti and 78–125% for K and S). The new methodology can be constructive in building a new database on Si and some other elements in biofuel plant varieties.