The Hadean surface was mainly covered by three kinds of rock: komatiite, KREEP basalt, and anorthosite, which were remarkably different from those on the modern Earth. Water–rock interactions between these rocks and water provided a highly reducing environment and formed secondary minerals on the rock surface that are important for producing metallo-enzymes for the emergence of primordial life. Previous studies suggest a correlation with active sites of metallo-enzymes and sulfide minerals based on an affinity with their structure, but they do not discuss the origins of metallic elements contained in these minerals, which are critical to understand where primordial life was born. Secondary minerals formed through water–rock interactions of komatiite in a nuclear geyser system are investigated, followed by a discussion of the relationship between active sites of metallo-enzymes and secondary minerals. Instead of komatiite, we used serpentinite collected from Hakuba Happo area, Nagano Prefecture in central-north Japan, which is thought to be one of the Hadean modern analogues for the birthplace of life. Several minor minerals were found, including magnetite, chromite, pyrite, and pentlandite, in addition to the major serpentine minerals. Pentlandite is not been mentioned in previous studies as a candidate for supplying important metallic elements to form metallo-enzymes in previous studies. It also acts as a catalyst for hydrogen generation, because it closely resembles the structural features of an active site of hydrogenases. Nickel-iron sulfide, pentlandite, is considered to be one of the important minerals for the origin of life. In addition, what kinds of minor mineral would be obtained from water–rock interactions of these rocks is estimated using a thermo-dynamic calculation. KREEP basalt contains large amounts of iron, and it could be useful for producing metallo-enzymes, especially for ferredoxins, an electron transfer enzymes associated with the emergence of primordial life.