To assess the preservation of the nitrogen isotope composition in reef corals, nitrogen isotopes in a well-preserved Pliocene fossil coral (located in the Tartaro formation on Luzon Island, Philippines (14°N, 121°E)) and in a modern coral (Kochi, Japan (32°N, 132°E)) were analysed using stepwise heating methods. The thermal decomposition of aragonite triggered the largest release of nitrogen at 700 °C for the modern coral and 550 °C for the Pliocene coral. The highest rate of nitrogen gas emission occurred at the aragonite collapse temperature, indicating that organic nitrogen was bound within the intra-crystals of coralline aragonites in both corals. After the aragonite collapsed in both corals, the nitrogen isotope ratios increased due to fractionation and then decreased to values similar to those observed in bulk samples of the modern (+ 10.1%) and Pliocene (+ 4.4%) corals. These results suggested that fresh organic nitrogen was released due to the decomposition of the internal skeletal structure at higher temperatures (900–1000 °C). Nitrogen isotopes in coral skeletons were preserved in intra-crystal aragonite, even in a Pliocene fossil, and stepwise heating methods were shown to be useful for determining the preservation of coralline nitrogen isotopes.