Mycotoxins are toxic mold metabolites that can adversely affect human and animal health. More than 400 mycotoxins have been identified so far. Cereals and nuts are the predominant mycotoxin-contaminated foodstuffs. Plant-based drinks produced from cereals, nuts, and legumes have grown in popularity. The mycotoxins accumulated in these crops may transfer to these beverages. A liquid chromatography–tandem mass spectrometry method was developed and optimized for the assessment of 22 mycotoxins in commercially available plant-based drinks in Latvia and Lithuania. A total of 64% of the seventy-two analyzed beverages were positive for one to sixteen mycotoxins, with deoxynivalenol, beauvericin, and enniatins A, B, B1, T-2, and HT-2 toxins detected most frequently. The European Commission has not yet set guidelines for the maximum mycotoxin concentrations in plant-based beverages, nor has the European Food Safety Authority conducted a risk assessment. Therefore, acute exposure studies were provided for the Latvian population based on the assumed replacement of dairy milk with plant-based beverages to ascertain the safety of plant-based milk substitutes. Based on the observed levels of mycotoxin prevalence and contamination levels and assumed exposure, it can be concluded that tested plant-based beverages may be relatively safe. However, exposure to emerging mycotoxins should be considered.