Although water-based paint is increasingly being advocated as environmentally friendly, it is more susceptible to biodeterioration during processing, preparation, and storage. Therefore, sufficient proactive measures are urgently needed to control and prevent microbial contamination along the production chain. The experimental setup comprised the investigation of the paints (e.g., pH, water content, FTIR) as well as the isolation and identification of bacterial and fungal contaminants via Sanger sequencing and MALDI-TOF MS. We identified well-known paint degraders such as Bacillus and Pseudomonas spp., however also less frequently abundant species like Rhodococcus. While the diversity within gram-negative bacteria turned out to be higher compared with gram-positive ones, the latter were predominant in paint and their immediate ambience, indicating that they are more resistant toward the applied measures. Our results emphasize the need for manufacturers to apply tailored measures against paint spoilage as a prerequisite for further product- and production-specific preservation concepts.