Rice terraces in Cordillera, Philippines, a world cultural heritage site, are threatened by the risk of collapse. It is crucial to manage these rice terraces for their conservation, while simultaneously practicing traditional farming. We examined the soil environment and investigated its effects on rice terrace conservation, by focusing on the hardpan condition; infiltration process, which is related to the collapse of rice terraces; and soil nutrition conditions in these sites. Field survey and soil analysis revealed that in areas where the hardpan was not sufficiently developed and water infiltration was effectively suppressed, organic matter content was significantly high, suggesting organic matter clogging. In these rice terraces, the amounts of P, K, Ca, and Mn were significantly low, showing the mineral leaching under reductive soil conditions. Therefore, hardpan formation, rather than organic matter clogging, is essential for the suppression of infiltration and prevention of potential terrace collapse. Because hardpan formation or organic matter clogging cannot be identified from the surface of flooded rice paddies, it is difficult to identify the influencing factor. Thus, we suggest that the hard soil layer should be checked before the planting season and drainage is allowed after the cropping season in the rainy season.