SUMMARY: AlphaPulldown2 streamlines protein structural modeling by automating workflows, improving code adaptability, and optimizing data management for large-scale applications. It introduces an automated Snakemake pipeline, compressed data storage, support for additional modeling backends like UniFold and AlphaLink2, and a range of other improvements. These upgrades make AlphaPulldown2 a versatile platform for predicting both binary interactions and complex multi-unit assemblies. AVAILABILITY AND IMPLEMENTATION: AlphaPulldown2 is freely available at https://github.com/KosinskiLab/AlphaPulldown. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.