To me, it seems like they are both just fermented soy beans, with the result being mostly glutamate with a bad smell. Soy sauce seems to be just the water that miso was left to steep in.
Yes, and no. Soy sauce could be said to be a by-product of miso. It can also be said to be a way to use “spoiled” miso. As step 2 for both products differs:
- Both start out with the same aerobic (“with air”) fermentation process, using the same mold and milk acid fermenting (“lactobacillus“) cultures.
- But for miso, this process is stopped before the mold sporulates, while for soy sauce, it is stopped right after it sporulated. (Which would be bitter, spoiled miso.)
Note that for organisms, from fungi to plants to animals, the act of making offspring (like spores) often causes drastic changes, which can wildly alter the chemical composition. Another example of this is is how flowering plants put all their resources in the most important part of them: Their flowers. So if you harvest them after they flower, they may be much less flavorful.
- For miso, it is put in anaerobic (“air-free”) conditions. Of course it won’t make spores with no air to spread them around. But it also causes a very different fermentation. It is like the difference between making bread (airy fermentation makes CO₂) and alcohol (air-free fermentation makes ethanol).
After that, it is essentially done, and it will continue to ferment if possible, whether it’s aging at the factory or in a jar on your shelf.
- While for soy sauce, it is then mixed with salt water and regularly stirred, keeping it fermenting aerobic and with a bigger focus on killing organisms that can’t tolerate salt, before it is filtered to leave only the liquids, and most of the time pasteurized. That makes it shelf-stable too. (Unpasteurized soy sauce is available though.)
So in essence, the differences are sporulation and air, or even more compact: The life that those fermenting organisms had was quite different. So their bodies and poop (which is what that lactic acid and alcohol literaly are) tastes quite different too.
TL;DR: Miso is to soy sauce what beer is to sourdough. :)