This dataset contains the IDA Indoor Climate and Energy (IDA ICE) simulation models used in the research article "Benchmarking Danish, Estonian and Finnish NZEB requirements with European Commission recommendations in residential and office buildings." The models represent three distinct building types: a new office building, an apartment building, and a single-family house. Each building was initially designed to comply with the respective national Nearly Zero-Energy Building (NZEB) requirements of Denmark, Estonia, or Finland. The primary purpose of these models was to systematically compare NZEB requirements and energy calculation methodologies across these three countries and against European Commission (EC) recommendations (EU 2016/1318). The simulations accounted for varying climatic conditions (using country-specific Test Reference Years and climate-corrected U-values based on heating-degree-days), national calculation methods, and standardized EN 16798-1:2019 input data. The models facilitate detailed dynamic simulations to analyze energy balance, primary energy (PE) consumption, and the impact of different Primary Energy Factors (PEFs). They were used to benchmark national NZEB performance levels, assess alignment with EC NZEB PE thresholds for Nordic and Oceanic climates, and investigate the influence of methodological discrepancies on building energy performance outcomes. The dataset supports the reproducibility of the study's findings and allows for further investigation into NZEB strategies in these regions.