The surface of Hadean Earth was mainly covered with three types of rocks—komatiite, KREEP basalt and anorthosite—which were remarkably different from those on the modern Earth. The water-rock interaction between these rocks and water provided a highly reducing environment and formed secondary minerals on the surface of the rocks that are important for producing metallo-enzymes for the emergence of primordial life. Previous studies suggested a correlation between the active site of metallo-enzymes and sulfide minerals based on the affinity of their structures, but they did not discuss the origin of metallic elements contained in these minerals which is critical to understanding where life began. We investigated secondary minerals formed through water-rock interactions of komatiite in a subaerial geyser system, then discussed the relationship between the active site of metallo-enzymes and secondary minerals. Instead of komatiite, we used serpentinite collected from the Hakuba Happo area, Nagano Prefecture in central-north Japan, which is thought to be a modern analog for the Hadean environment. We found several minor minerals, such as magnetite, chromite, pyrite and pentlandite in addition to serpentine minerals. Pentlandite has not been mentioned in previous studies as one of the candidates that could supply important metallic elements to build metallo-enzymes. It has been shown to be a catalyst for hydrogen generation possibly, because of structural similarity to the active site of hydrogenases. We consider the possibility that nickel-iron sulfide, pentlandite, could be important minerals for the origin of life. In addition, we estimated what kinds of minor minerals would be obtained from the water-rock interaction of these rocks using thermodynamic calculations. KREEP basalt contains a large amount of iron and it could be useful for producing metallo-enzymes, especially ferredoxins—electron transfer enzymes, which may have assisted in the emergence of life.