The shortage of data on non-intentionally added substances (NIAS) present in food contact material (FCM) limits the ability to ensure food safety. Recent strategies in analytical method development permit NIAS investigation by using chemical exploration, but this has not been sufficiently investigated in risk assessment context. Here, exploration is utilized and followed by risk prioritization on chemical compounds that can potentially migrate to food from two paperboard FCM samples. Concentration estimates from exploration are converted to tentative exposure assessment, while predicted chemical structures are assessed using quantitative structure-activity relationships (QSAR) models for carcinogenicity, mutagenicity, and reproductive toxicity. A selection of 60 chemical compounds from two FCMs is assessed by four risk assessors to classify compounds based on probable risk. For almost 60% of cases, the assessors classified compounds as either high priority or low priority. Unclassified compounds are due to disagreements between experts (18%) or due to a perceived lack of data (23%). Among the high priority substances are high-concentration compounds, benzophenone derivatives, and dyes. The low priority compounds contained e.g. oligomers from plasticizers and linear alkane amides. The classification scheme provides valuable information based on tentative data and is able to prioritize discovered chemical compounds for pending risk assessment.