The present invention provides an in-line system for milling sorbent material to be used in a pneumatic conveying system. The system provides for optimal particle size in a duct injection system, regardless of the original sorbent particle size, and is designed to prevent clogging of the milled material through the system. Methods of operation for milling, as well as cleaning the mills while providing various sorbent material by-pass configurations to minimize system down-time while enhancing material throughput and that support the unique aspects of the system, are also described in detail below.