Gluten-free cereal products have grown in popularity in recent years as they are perceived as “healthier” alternatives and can be safely consumed by celiac patients, and people with gluten intolerance or wheat allergies. Molds that produce mycotoxins contaminate cereal crops, posing a threat to global food security. Maximum levels have been set for certain mycotoxins in cereal flours; however, little is known about the levels of emerging mycotoxins in these flours. The aim of this study was to develop an efficient, sensitive, and selective method for the detection of four emerging (beauvericin and enniatins A1, B, and B1) and three regulated (aflatoxin B1, zearalenone, and deoxynivalenol) mycotoxins in gluten-free flours. Ultrasound-assisted matrix solid-phase dispersion was used in the extraction of these mycotoxins from flour samples. The validated method was utilized for the LC-MS/MS analysis of conventional and organic wholegrain oat and rice flours. Six of the seven target mycotoxins were detected in these samples. Multi-mycotoxin contamination was found in all flour types, particularly in conventional wholegrain oat flour. Despite the low detection frequency in rice flour, one sample was found to contain zearalenone at a concentration of 83.2 μg/kg, which was higher than the level set by the European Commission for cereal flours. The emerging mycotoxins had the highest detection frequencies; enniatin B was present in 53% of the samples at a maximum concentration of 56 μg/kg, followed by enniatin B1 and beauvericin, which were detected in 46% of the samples, and at levels reaching 21 μg/kg and 10 μg/kg, respectively. These results highlight the need to improve the current knowledge and regulations on the presence of mycotoxins, particularly emerging ones, in gluten-free flours and cereal-based products.