Modern large-scale I/O applications that run on HPC infrastructures are increasingly becoming metadataintensive. Unfortunately, having multiple concurrent applications submitting massive amounts of metadata operations can easily saturate the shared parallel file system's metadata resources, leading to unresponsiveness of the storage backend and overall performance degradation. To address these challenges, we present PADLL, a storage middleware that enables system administrators to proactively control and ensure QoS over metadata workflows in HPC storage systems. We demonstrate its performance and feasibility by controlling the rate of both synthetic and realistic I/O workloads. Results show that PADLL can dynamically control metadata-aggressive workloads, prevent I/O burstiness, and ensure I/O fairness and prioritization.