The dataset ‘Heat stored in the Earth system: Where does the energy go?’ contains a consistent long-term Earth system heat gain over the past 58 years. Human-induced atmospheric composition changes cause a radiative imbalance at the top-of-atmosphere which is driving global warming. This Earth Energy Imbalance (EEI) is a fundamental metric of climate change. Understanding the heat gain of the Earth system from this accumulated heat – and particularly how much and where the heat is distributed in the Earth system - is fundamental to understanding how this affects warming oceans, atmosphere and land, rising temperatures and sea level, and loss of grounded and floating ice, which are fundamental concerns for society. This dataset is based on a study under the Global Climate Observing System (GCOS) concerted international effort to update the Earth heat inventory, and presents an updated international assessment of ocean warming estimates, and new and updated estimates of heat gain in the atmosphere, cryosphere and land over the period 1960-2018.