Heritage restoration of historic monuments involves specific challenges for its implementation. In this scenario, archaeological work is a fundamental part of that legal, conservation, and community process. We present the results of the documentation and archaeological excavations carried out beneath the floor of the centenarian Church of San Juan (Dalcahue, Chiloe) and the San Juan 1 archaeological site in the western Patagonian archipelago. Historical burials (ca. 280 to 140 cal years BP) and diverse archaeological materials recovered from sedimentary matrices that resulted from a succession of occupations by marine hunter-gatherers (from ca. 6.000 BP) constitute a set of information that supports the cultural sequence of the area. Thus, the bioanthropological, ceramic, lithic, archaeofaunistic, and historical analyses inform us about the subsistence of human groups and part of the technological assemblages used and discarded both in pre-Hispanic and historical times at Chiloe island. We expect that the example set in this work contributes to future restoration and enhancement strategies that respect historical and contemporary uses of various heritage sites.