The site of Iita in northwestern Greenland had near-continual occupation from 1000 CE to the mid-20th century, which presents an unparalleled opportunity to examine diachronic changes in the use of marine mammals for food and raw material resources by Pre-Inuit (Late Dorset) and Inuit-Inughuit—two culturally distinct Indigenous groups. Limited wood in High Arctic environments necessitated the use of antler, bone, and ivory for tool making. Choices in the selection and processing of osseous material reflect changes in the way these two groups used the same resources. However, modification of osseous material during the tool-making process is often to such an extent that few diagnostic features remain for species identification. Here, we include Zooarchaeology by Mass Spectrometry (ZooMS) to identify typically indeterminate pieces of manufacturing debris from preserved collagen. The minimally destructive extraction technique using polishing films had a 99% success rate. The results suggest that the selection of raw materials from certain marine mammals, particularly narwhal, by toolmakers at Iita was more frequent than previously understood through traditional faunal analysis alone. There is a paucity of narwhal from the Pre-Inuit (Late Dorset) assemblage, which contrasts starkly with the high frequency of narwhal in the Inuit-Inughuit assemblage. We demonstrate the importance of combining the analysis of bone-tool manufacturing debris with traditional dietary faunal remains to improve our understanding of resource use in coastal environments.