In this work, the crosslinking reaction of partially carbonated epoxidized soybean oils with different diamines was investigated. To this end, a series of carbonated soybean oils (CSBO), with a carbonation ratio ranging from 45% (CSBO45) to 98% (CSBO98) were synthesized by CO₂ carbonation of epoxidized soybean oil (ESBO). The relative aminolysis rate of the carbonate and epoxide functions of CSBO45, and also of the esters of the triglyceride skeleton, was monitored through an unprecedented combination of in situ infrared and Raman spectroscopy at various temperatures T (60 °C ≤ T ≤ 150 °C). Interestingly, two regimes are identified: (i) for T < 100 °C, a PHU regime, during which all the carbonate functions of CSBO45 react to provide an uncrosslinked PHU prepolymer (viscous liquid), (ii) for T ≥ 100 °C, a hybrid regime, during which the epoxide functions react to provide a hybrid thermosetting polymer (elastic solid). For the first time, we report the “conversion vs. time” plots for the aminolysis of epoxide in ESBO and partially carbonated ESBO. They indicate that the initiation of the reaction is thermally delayed as compared to the aminolysis of the corresponding carbonates. Surprisingly, the sol–gel transition of CSBO45 is correlated to the initiation of epoxide aminolysis, a counterintuitive conclusion given that ESBO cannot be crosslinked by a diamine under the same conditions. These results suggest that the combination of reactive carbonates with sluggish epoxides results in a decrease of undesirable side reactions such as ester aminolysis and intramolecular cyclization. Finally, general guidelines can be recommended for the stepwise synthesis of triglyceride-based hybrid poly(hydroxyurethane) thermosets.