Sauté the onions in olive oil in a large, deep skillet over medium heat until translucent, about 3-4 minutes. This forms the flavor foundation of your stroganoff.
Add the minced garlic and cook for another 30 seconds until fragrant, being careful not to burn it as this will create bitterness.
Increase the heat to medium-high and add the mushrooms. Cook them without stirring too frequently (about 5-7 minutes) to allow them to release their moisture and then brown. This is crucial for developing deep flavor.
Stir in the tamari/soy sauce, paprika, thyme, and black pepper, allowing the mushrooms to absorb these flavors for about 1 minute.
Sprinkle the flour over the mushroom mixture and stir continuously for 1 minute to cook out the raw flour taste and create a thickening base.
Pour in the vegetable broth slowly while stirring to prevent lumps from forming. Bring the mixture to a gentle boil.
Add the uncooked pasta directly to the pot and stir to combine. Reduce heat to medium-low, cover, and simmer for 10-12 minutes, or until the pasta is al dente and most of the liquid has been absorbed.
Remove the pot from heat and stir in the plant-based sour cream and nutritional yeast until completely incorporated. Let it sit for 2 minutes to thicken slightly.
Taste and adjust seasonings as needed, adding salt or more tamari if desired for depth of flavor.
Serve hot, garnished with fresh parsley and an extra dollop of plant-based sour cream if desired.