Tempe is a fermented soybean food from Indonesia, made by inoculating Rhizopus spp. onto cooked and dehulled soybean. Tempe has been a part of Indonesian culture since the 16th century and is now produced globally as a highly nutritious plant-based food. Despite a longstanding history on the production of tempe, very few studies have been reported to understand the effect of raw material to the end product metabolite composition. In this research, we applied GC/MS-based metabolite profiling to investigate the effect of various possible factors that might affect the final product (environmental factors, raw materials, and starter cultures). Representative samples were tempe produced by Indonesian industries, Japanese industries as well as laboratory made tempe. The results showed that both environmental factors and raw materials (soybean, water, and starter culture) contributed to the tempe metabolite profile. Here we found the possibility that starter cultures might play a greater role to determine the metabolite profiles compared to other tested factors. This research might provide useful insights for the larger scale industries to maintain the quality of tempe for the benefit of the consumers.