In a small saucepan, combine soy sauce, sugar, water, apple cider vinegar, garlic and red pepper flakes (everything except nutritional yeast and honey). Bring to a boil; reduce heat to simmer.
Remove 2 tablespoons sauce to a small bowl and whisk in nutritional yeast. Return to the saucepan and continue simmering until the sauce thickens slightly, about 10 minutes.
Stir in honey and cook for a few more minutes. Remove from heat and cool to room temperature, or cover and refrigerate for up to one week. Bring to room temperature before using.