Soil micromorphology was among the approaches used to explore site formation in two cave sites in northern Luzon: Eme and Dalan Serkot Caves. Interplay of biogenic, sedimentary, and anthropogenic processes worked and reworked the archaeological sediments at both sites. Eme Cave was found to be highly bioturbated by faunal activities and shrink-swell processes, and caution is needed in interpreting its archaeological contexts. However, thin section study revealed wood ash and possible burnt soil fragments, along with charcoal, attesting to later prehistoric burning activity at the site at some time. In Dalan Serkot Cave, along with standard cave sediments a volcanic ash deposit was identified, apparently deposited before 6200 b.p., that must have affected local communities, and that could be used as a stratigraphic marker for future research in the area.