Cut the spaghetti squash in half, widthwise so it will fit into the Instant Pot (IP). (For oven directions see notes.)
Scoop out the seeds with a spoon or your hands. Add the steamer basket to the IP and then 1 cup of water. Fit the spaghetti squash inside the IP.
Lock the lid and set the valve to “Seal.” Click the “Manual” button and hit the “+” sign until it is at 7 minutes.
While the squash is cooking, add 1 TBS oil to an oven safe sauté pan over medium high heat. Add the sliced mushrooms. Brown on each side for 3-5 minutes (to caramelize the mushrooms for depth of flavor).
Add the carrots and onion. Saute for an additional 5 minutes.
Once the squash is done, let the pressure come down manually (I usually wait about 10 minutes). Then, push the valve to venting and open the IP. With a fork scrap the flesh of the squash into spaghetti strands. Discard the skin of the squash.
Add the squash to the saute pan with the vegetables.
Add the marinara sauce, salt, pepper and red pepper flakes.
Mix until combined and let cook for 3-5 minutes. Taste and add additional salt if needed.
Optional: turn on broiler in oven. Sprinkle shredded parmesan cheese/mozzarella all over spaghetti squash mixture.
Place skillet under broiler until cheese is melty and bubbly, about 3-5 minutes.