Traditional canary seed (Phalaris canariensis L.) has a high nutritional value and protein content, standing out for its tryptophan, cysteine, and phenylalanine content and for being gluten-free. These characteristics position it as a raw material with potential for the development of foods intended for human consumption. However, the varieties cultivated in Argentina have amorphous silica spicules in their hulls, which are potentially carcinogenic, limiting their use in food and requiring technological treatments to reduce or eliminate them. In this context, the objective of the present work was to evaluate the application of hydrothermal and microwave pretreatments to traditional canary seed grains to minimize spicules in the resulting flour. The studies were conducted by combining hydrothermal pretreatment (110°C, 1 atm, 15 min) followed by microwave exposure at three times (30 s, 60 s, and 120 s). The pretreated samples were then subjected to an abrasive treatment (1h, 175 rpm) in a specially designed equipment and a subsequent dehulling stage (pilot impact dehuller: 2960 rpm, 40 s). Finally, the samples were ground in a blade mill to obtain the flours. Spicules quantification was carried out using a microscope (Ernsleitz Wetzlar, Germany, 200X magnification) in previously calcined samples (550°C, 4 h) to avoid interference. The results obtained showed significant differences (Tukey, p < 0.05) at 120 s of microwave exposure compared to shorter times. Under these conditions, a reduction in spicules from 843.4 ± 66.7 spicules/g of flour (dry basis, d.b.) to 27.6 ± 13.6 spicules/g of flour (d.b.) was achieved. These results show that the combined application of hydrothermal and microwave pretreatments could reduce the presence of spicules in traditional canary seed flours, expanding their use in foods intended for human consumption.