In an era marked by frequent budgetary changes and staff turnover, understanding how these fluctuations impact bureaucratic capacity is crucial. Utilizing more than 20 million personnel records from 2011 to 2023, we estimate a capacity index at the subagency (bureau) level for over 650 units using autoencoder methods. Our findings provide empirical evidence that the degree of ideological misalignment between the president and agencies is positively correlated with agency capacity. Additionally, this capacity index can serve as either an independent or dependent variable in other studies on bureaucratic politics. Methodologically, the generation of our measures offers a novel approach for handling mega-sized datasets, which can be adapted to other contexts.