Advances in detection technologies are essential for creating a safer and more transparent food system. Recently, digital PCR has arisen as a newsworthy alternative to real-time PCR for plant species detection in processed and complex foods. Thus, we conducted two case studies: The detection of sesame (Sesamum indicum) as an allergenic food and the identification and quantification of bacopa (Bacopa monnieri) in plant food supplements for botanical authentication purposes. In a commercial set of samples, nanoplate digital PCR (ndPCR) approaches exhibited optimal sensitivity, acceptable performance parameters and robustness. The present work demonstrates the applicability of ndPCR for the detection of allergenic food ingredients and botanical species in complex and processed matrices for the first time, emphasizing this technique as a novel sensitive and specific tool to verify labeling compliance. Here, I present our methods and results.