Plant-based milk alternatives can be produced from a variety of raw materials. The microbial load of the used raw materials can vary greatly, affecting the heating parameters necessary for reducing the microbial load. In this study, plant-based raw materials for producing oat-, almond-, pea-, and rice-based drinks were examined for their microbial load. In this context, flours, flakes, protein isolates, and syrups were tested. The microbiological tests included i) the mesophilic viable cell count (mVCC), ii) the thermophilic viable cell count (tVCC), iii) the mesophilic spore count (mSC), and iv) the thermophilic spore count (tSC). Pure cultures were isolated from each sample, and bacterial species were identified using 16S rRNA gene analysis. The plant-based raw materials (oat, almond, pea and rice) showed wide variations in the viable cell and spore count, ranging from 1 to 8.5 log10 CFU/g. Most of the raw materials contained a high proportion of spores in the viable cell count. Despite previous ultra-high temperature treatment (UHT treatment), the oat and rice syrups showed spore levels of 1 to 4 log10 CFU/g. In total, 435 bacterial isolates were classified with the most frequent species belonging to the genus Bacillus. Among these, B. licheniformis, B. subtilis, and B. tequilensis were the most prevalent. However, other species such as B. cereus, B. amyloliquefaciens, P. etheri, and G. stearothermophilus were also present. Based on the initial spore load of the raw materials, the required effect of the heat treatment B* can be calculated to ensure a commercially sterile plant-based drink. For an average mesophilic bacterial load of oat flours with 5 log10 CFU/g, a 12 log10 reduction is required and for a higher contamination with 9 log10 CFU/g a 16 log10 reduction is already necessary.