In Australia, widespread evolution of multi-resistant weed populations has driven the development and adoption of harvest weed seed control (HWSC). However, due to incompatibility of commonly used HWSC systems with highly productive conservation cropping systems, better HWSC systems are in demand. This study aimed to evaluate the efficacy of the integrated Harrington Seed Destructor (iHSD) mill on the seeds of Australia’s major crop weeds during wheat chaff processing. Also examined were the impacts of chaff type and moisture content on weed seed destruction efficacy. Initially, the iHSD mill speed of 3,000 rpm was identified as the most effective at destroying rigid ryegrass seeds present in wheat chaff. Subsequent testing determined that the iHSD mill was highly effective (>95% seed kill) on all Australian crop weeds examined. Rigid ryegrass seed kill was found to be highest for lupin chaff and lowest in barley, with wheat and canola chaff intermediate. Similarly, wheat chaff moisture reduced rigid ryegrass seed kill when moisture level exceeded 12%. The broad potential of the iHSD mill was evident, in that the reductions in efficacy due to wide-ranging differences in chaff type and moisture content were relatively small (≤10%). The results from these studies confirm the high efficacy and widespread suitability of the iHSD for use in Australian crop production systems. Additionally, as this system allows the conservation of all harvest residues, it is the best HWSC technique for conservation cropping systems.