Spaghetti Squash Au Gratin: The Backstory (And a Tangent...)

Alright, so here’s the thing. The first time I made Spaghetti Squash Au Gratin, I was half-convinced it would turn out like something a rabbit would politely pass over (long story about a family holiday potluck, remind me to tell you another time). But somewhere between the stringy squash and the oozy cheese, it kinda grew on me. And actually, my kids started calling it "the cheesy spaghetti pumpkin." That’s stuck.

Also, I once dropped a hot spaghetti squash on the floor, so now I always use an oven mitt. Safety first, but also, don’t let anyone fool you into thinking this dish is just a lighter stand-in for potatoes au gratin. It's delicious in its own right. OK, enough gabbing. Onwards!

Why I Keep Coming Back to This

I make this whenever I want comfort food without the heavy, post-dinner "why did I do that?" feeling. My family goes a bit bonkers for it—mainly because a) cheese, and b) it’s fun to pull the golden top off. My eldest always races me for the corner piece. Sometimes I use this recipe as an excuse to clear out cheese odds and ends from the fridge, which, let's be honest, is kind of a win. (Also, once I tried making it on a weeknight and thought I could just zap the squash in the microwave to speed things up—not my finest idea, but hey, edible is better than nothing!)

What You’ll Need (…ish)

1 medium spaghetti squash (sized somewhere between a rugby ball and a fat kitten; about 2-3 lbs)
2 tablespoons olive oil (or a big glug—don’t stress it)
½ large yellow onion, chopped (I sometimes throw in a shallot for extra oomph, or just skip if I have none…)
2-3 cloves garlic, minced (or a spoonful of the jarred stuff if you’re in a rush)
½ cup Greek yogurt (granny swore by sour cream but, honestly, both are good)
1 cup shredded sharp cheddar (the sharper the better—I use whatever’s on sale)
½ cup grated parmesan (or Grana Padano if you’re feeling fancy)
½ teaspoon salt (unless your cheese is already very salty—then maybe less)
¼ teaspoon pepper (honestly, I just eyeball this)
Pinch red pepper flakes (optional; I like the kick, the kids claim I’m sabotaging them)
2 tablespoons chopped chives or parsley (if you remember—most days I forget and just use dried)

How I Actually Make It (No Judgment)

First, preheat your oven to 400°F (200°C). Stab the spaghetti squash all over with a fork, like you’re making battle plans. Place on a baking sheet and bake for about 40–50 minutes, until you can poke it easily with a fork. Or you can microwave it for about 10–12 minutes if you’re short on time, but it gets a bit mushy. Your call.
Once it’s cool enough to handle (read: not lava), slice the squash open. Scoop out the seeds (a surprisingly gross bit, but also kind of fun), then use a fork to shred those magical spaghetti-like strands into a big bowl. Sometimes mine come out in clumps—don’t sweat it.
Meanwhile, heat olive oil in a skillet over medium heat, add the chopped onions and sauté until they’re soft and smelling irresistible. Chuck in the garlic too; I always forget and add it a little late, but just don’t let it burn. It’s fine if you do, really.
Turn off the heat and mix in the Greek yogurt (or sour cream) with the onions and garlic. Add the cooked squash strands, ¾ of the cheddar, about half your parmesan, salt, pepper, and chili flakes. Give it a good stir—this is where I usually sneak a taste (for science, obviously).
Scoop everything into a casserole dish (any oven-safe pan works; once I used a pie plate and nothing exploded). Sprinke on the rest of the cheese and parmesan. Scatter chives or parsley because it looks fancy.
Bake at 400°F for about 20-25 minutes, or until it’s bubbling and that cheesy top is golden brown. I crank the broiler on at the end for a minute or two for extra toasted cheese (do NOT walk away, trust me—I have the crispy-black cheese experience to prove it).

What I’ve Learned (AKA My "Oops" Notes)

Don’t overcook the squash or you get watery gratin. I tend to drain the strands in a colander for a minute or two. One time I forgot, and we basically had cheese soup. Still tasty, but…
If you swap Greek yogurt for full-fat sour cream, it’s a little richer (in a good way!).
It’s fine if the top gets kind of unevenly gold—just pretend it’s rustic and intentional.

Variations I’ve Messed With

Add cooked bacon or pancetta—pretty epic but my vegetarian friend Sarah draws the line there.
Swap the cheddar for gouda or fontina—makes it gooier, but sometimes a little bland. Now, blue cheese? Tried it once, wouldn’t do it again. Yikes.
A friend of mine stirs in spinach sometimes. Actually, that works nicely.

Stuff You Might Need (But Don’t Panic)

Baking sheet (or, in a pinch, just layer foil right on your oven rack; I do not recommend but hey, it works in a crisis)
Medium skillet (nonstick makes cleanup easier, but use what you have)
Casserole dish or pie plate
Fork and sharp knife (trust me, be careful with that squash—it’s like wrestling a bowling ball)

Keeping Leftovers (…If You Have Any)

Store any leftovers in an airtight container in the fridge. Technically, it’ll keep for 3 days, probably a bit longer. But honestly, in my house it’s gone after breakfast the next day. Cold gratin straight from the dish? Don’t judge.

How We Serve It (or: Dinner Table Debates)

I like serving this right out of the baking dish, family-style. Sometimes it’s a stand-alone dinner, other times I make it a cheesy side for roast chicken (here’s a super helpful method I use: serious eats roast chicken guide). My mom, of course, insists it must be paired with a big green salad, and she’s probably right—I just never remember to actually make the salad until it’s too late.

Pro Tips I Wish Someone Had Told Me

Don’t try to rush roasting the squash by cranking up the heat. I tried 450°F once. Result: burnt edges, raw center. Not worth it.
At first I used pre-shredded cheese. But grating your own (or letting a helper do it!) makes it melt so much nicer.
If you’re worried about watery squash, just squeeze the strands gently in a clean kitchen towel. I always forget, then remember midway through. Oops.

FAQ: Stuff People Have Actually Asked Me

Do you taste the squash much?: Not really. It’s got a subtle flavor, but mostly this dish tastes like cheesy, oniony comfort. So yeah, if you hate squash, you might notice, but otherwise it’s just cozy food.
Can I freeze it?: Honestly, I tried once and it got all watery when thawed—probably wouldn’t recommend. Eat it fresh, or just have really cheesy lunch leftovers tomorrow.
Does this feed a crowd?: One squash makes enough as a side for 4 to 6 folks—unless you’ve got hungry teens, in which case, double it (seriously, I learned that the hard way!).
What’s the best cheese mix?: I lean sharp cheddar and parmesan, like Cabot or the house brand from Aldi (both work), but honestly, this is one of those "use up your cheese bits" recipes. There's no bad answer here!
Got any side ideas?: I sometimes just do crusty bread and a salad, simple and good. For fancier nights: this easy arugula salad is a nice match. Or just wine and a fork—works, too.

So that's my real-life, lived-in approach to Spaghetti Squash Au Gratin. If you try it with a weird cheese or a sneaky veggie, let me know how it goes (unless it's blue cheese, that's on you!).

Spaghetti Squash Au Gratin Recipe