3D electron diffraction (3D ED) data of griseofulvin (GSF) inclusion complex with polyethylene glycol (PEG) form I (GSF IC-I) collected automatically using software EPU-D at 100 K on a ThermoFisher Titan Krios (300 kV) equipped with a CETA-D detector. A total of 231 datasets were collected from a sample containing multiple phases of GSF in 2 days. Crystal identification and selection were performed by an operator while 3D ED data collection was carried out fully automatically. Data was processed automatically by software package edtools (https://doi.org/10.5281/zenodo.6953489) using XDS (https://doi.org/10.1107/S0907444909047337). A hierarchical clustering analysis (HCA) algorithm implemented in edtools was used to cluster the datasets belonging to the same phase through the Euclidean distance between the unit cell parameters. Out of the 231 datasets collected, 15 datasets were idneitified to be the GSF IC-I phase.