According to some embodiment, a backup storage system receives, by a first phase of a data deduplication pipeline, a request from a client for reading or writing a data segment associated with a data stream stored in or to a storage system. In response to the request, the system retrieves, by the first phase, load parameters associated with a second phase in the data deduplication pipeline. For each of the load parameters associated with the second phase, the system determines, by the first phase, whether the load parameter has exceeded a load threshold associated with the second phase. The system throttles, by the first phase, performance of a specific job in the data deduplication pipeline by the second phase in response to a determination that at least one of the load parameters associated with the second job phase has exceeded the load threshold associated with the second phase.