<p>The eastern Indonesian Seas acted as an Indo–Pacific interbasin heat capacitor given its deep topography profile and direct interaction with the Indonesian Throughflow (ITF). Thus, knowing how much heat is brought by the ITF retained by the area provides important information regarding the overall tropical ocean heat balance and possible repercussions on the climate system. This study investigated the upper 300 m heat content variabilities of the area (114°E–134°E; 8.25°S–1.75°S) from 1995 to 2022 through a closed heat budget analysis. It was found that the long-term heat buildup in the study area was solely driven by the accumulation of warmer-than-usual water from the western Pacific Ocean transported through the Makassar Strait, which resulted in a decadal trend of 0.85 × 10²¹ J decade^–1. The additional heat was not fully transmitted toward the Indian Ocean through heat transport in the ITF outflow, which induced only –0.19 × 10²¹ J decade^–1 of long-term trend to the study area. Other processes, which can be estimated in the heat budget analysis, also acted in discharging those additional heat. Despite being the dominant process behind the decadal trend, the heat transport variabilities in the Makassar Strait did not always govern the ocean heat content variation in the study area. The period between 2020 and 2022 provided an extreme example when the heat transport variabilities in Makassar Strait induced only a subtle amount of heat content anomalies. Instead, it was the heat transport modulation in the Halmahera Sea, which responsible for the rapid heat buildup during the 2020–2022. The results underline the source of long-term trend and variabilities of the ocean heat content which can be different.</p>