Some database systems may implement encryption services to improve the security of data stored in databases or on disks. The systems may implement encryption using multiple encryption keys. For example, a worker server may implement a system call interceptor, such as a filesystem in userspace (Fuse) driver. The system call interceptor may intercept system calls (e.g., associated with query or extract, transform, and load (ETL) jobs) as they enter or exit the kernel. The system call interceptor may determine whether data sets associated with the jobs are marked for encryption, and may perform an encryption process on the data sets. A worker may encrypt and store data sets on a worker disk or at a file store, or may retrieve and decrypt the data sets. The system may additionally manage encryption keys, and may provide mechanisms for archiving or revoking encryption keys while maintaining user access to stored data sets.