Papaya (Carica papaya L.) is widely cultivated in tropical and subtropical countries. While ripe fruit is a popular food item globally, the unripe fruit is only consumed in some Asian countries. To promote the utilization of unripe papaya based on the compositional changes of biological active metabolites, we performed liquid chromatography-Orbitrap-mass spectrometry-based analysis to reveal the comprehensive metabolite profile of the peel and pulp of unripe and ripe papaya fruits. The number of peaks annotated as phenolics and aminocarboxylic acids increased in the pulp and peel of ripe fruit, respectively. Putative carpaine derivatives, known alkaloids with cardiovascular effects, decreased, while carpamic acid derivatives increased in the peel of ripe fruit. Furthermore, the functionality of unripe fruit, the benzyl glucosinolate content, total polyphenol content, and proteolytic activity were detectable after heating and powder processing treatments, suggesting a potential utilization in powdered form as functional material.