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Paleo Spaghetti Squash Pastitsio, Greek Baked Ziti (AIP, Whole30, Low-carb)

4.27 from 67 votes

What’s Inside: Paleo Spaghetti Squash Pastitsio, AKA Greek Baked Ziti made with a creamy cauliflower bechamel sauce, perfectly spiced ground meat, and the recipe MVP… spaghetti squash! Make this decadent + comforting AIP-friendly dish.

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Dairy-free Bechamel) dairy-free, gluten-free, grain-free, low-carb, AIP-friendly via Food by Mars

Paleo Spaghetti Squash Pastitsio, Greek Baked Ziti (AIP, Whole30, Low-carb)

OPA! What the heck is Pastitsio?! Well, it’s a Greek baked pasta dish that consists of a creamy, cheesy bechamel sauce, ground beef or lamb, and of course pasta. It’s like a white baked ziti. When I first started trying authentic Greek food (not talking Diner food, here.) this became one of my absolute favorites. And I haven’t had it in years… once the dairy intolerance got a little too real, I had to part ways. Recently, my husband was eating it and one whiff set me on the road to making my own Paleo and AIP version. No dairy, no cheese, no gluten nor grains… and somehow the consistency, the creamy cheese-like flavor is the closest match I’m going to get. And I’m not complaining anymore because now I have Paleo Spaghetti Squash Pastitsio.

GUYS. When I say I patted myself on the back after tasting this, I’m not joking. And I’ve basically never done that before… no really, I didn’t even know I could bend like that.


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This ziti is different than the more well-known Greek Lasagna (or casserole), called Moussaka… which is also mega delicious. Check out my recipe for that one right here!

Easy, flavorful ingredients for Paleo Greek Baked Ziti:

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Dairy-free Bechamel) dairy-free, gluten-free, grain-free, low-carb, AIP-friendly via Food by MarsThe ground meat is MEGA flavorful. The cinnamon in here is a very Greek flavor. They love using cinnamon on meat and I fully concur. It’s fabulous. The onions give it a little sweetness, and it all comes together perfectly.

The spaghetti squash is the pasta replacement, and you will not miss it. Try making this in “rings” for a quick way to roast the squash without the sogginess factor!

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Dairy-free Bechamel) dairy-free, gluten-free, grain-free, low-carb, AIP-friendly via Food by Mars

How to make a Paleo Cheese Sauce?

And let’s not beat around the bush here, let’s talk bechamel. Bechamel sauce has to be one of the coziest, dreamiest satisfying sauces around. So I leaned on COCONUT CREAM and CAULIFLOWER to get the job done. With a few other odds and ends… this sauce was thick enough to coat the wooden spoon I used to stir it with, filled my kitchen with a cheese-like aroma and the color was spot on too. There’s no going back now, I can’t un-taste the sauce, folks. I will likely be making this Cauliflower Bechamel sauce on the regs.

Are you a cheese-lover who needs to cut back on dairy? Welcome! Be sure to check out this list of my best dairy-free cheese sauces for more variations.

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Dairy-free Bechamel) dairy-free, gluten-free, grain-free, low-carb, AIP-friendly via Food by MarsThese 3 components gel so well together, I was so stoked at the turnout. When I cut into the bubbly golden brown top I had deja vu, one taste of it and I was taking a trip down memory lane. Dates in Greek Tavernas in Astoria with my hubby when we were just two crazy kids in love… ah yessss – that’s the stuff!

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Dairy-free Bechamel) dairy-free, gluten-free, grain-free, low-carb, AIP-friendly via Food by MarsIf you’ve ever tried pastitsio, your jaw just might drop at this taste- & look-a-like. If you haven’t, I’m going to wager you’ve at least had a bechamel sauce and at least have had baked ziti, so it’s not too much of a stretch to imagine the magic that Pastitsio really is. And you will love this… make this your next Sunday dinner project and tell me all about it.


More Paleo Comfort Dishes

Video: Watch How To Make The Recipe

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Dairy-free Bechamel) dairy-free, gluten-free, grain-free, low-carb, AIP-friendly via Food by Mars

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Bechamel Sauce)

4.27 from 67 votes
This dreamy favorite is getting a dairy-, gluten-, grain-free makeover. Spaghetti squash makes for a low carb “pasta” dish and the cauliflower bechamel just might fool you!! (AIP-friendly)
Prep Time: 30 minutes
Cook Time: 40 minutes
Total Time: 1 hour 10 minutes
Yield: 6 people
Calories 537kcal


Spaghetti Squash (“Pasta”) Layer

  • 2 small-medium spaghetti squash (you'll need approx. 4-5 cups cooked)
  • 1 Tbsp extra-virgin olive oil

Ground Meat Layer

  • 2 Tbsp olive oil
  • 1 small yellow onion, chopped
  • 1 lb. grass-fed ground beef or lamb
  • 2 tsp dried oregano
  • 1 tsp sea salt
  • 2 tsp ceylon cinnamon
  • 2 tsp tomato paste (omit for AIP)
  • 3 cloves garlic minced

Dairy-free Cauliflower Bechamel Sauce

  • 2 cups cauliflower steamed
  • 1 cup coconut cream*
  • 2 Tbsp nutritional yeast**
  • 1/2 cup water
  • 2 Tbsp arrowroot starch/flour
  • 1/2 Tbsp lemon juice
  • 1/2 tsp sea salt

Nutritional Yeast-Cinnamon Topping

  • 2 Tbsp nutritional yeast flakes
  • 1-2 tsp ceylon cinnamon
  • 1 pinch sea salt


  • Prep an 8 in. baking dish (glass, ceramic or enamel), whatever you'd use for a casserole for example. Grease it lightly with coconut oil and set aside. Pre-heat oven to 350f degrees.

Spaghetti Squash (“Pasta”) Layer

  • Pre-heat oven to 400f degrees.
  • Cut squash into 1-inch "rings" and discard seeds.
  • Lightly drizzle olive oil on both sides of squash rings and bake on a parchment-lined baking sheet for approx. 30 mins, flipping half-way.
  • When done, remove from oven and set aside. Reduce the oven temperature to 350f degrees and grease an 8in. baking dish, set aside.

Ground Meat Layer

  • Chop onions small and set aside. Heat a skillet over medium heat and add the ghee/lard, let it melt. Once melted, toss the onions in the pan and using a wooden spoon, stir around, let cook for 3-5 minutes until translucent and soft.
  • Add ground meat and break up with your wooden spoon into small pieces, stirring with the onions. Sprinkle your seasonings over top and continue mixing. If using tomato paste, add in. Lastly, add the minced garlic so it doesn’t burn. 
  • Cook meat until the juices that release start to evaporate and no red meat remains. Taste the meat and season to your liking! When done, set aside.

Dairy-free Cauliflower Bechamel Sauce

  • In a pot, steam cauliflower florets with boiling water until it’s tender when pricked with a fork (approx. 8 mins.).
  • Make a "slurry" by combining the arrowroot starch with 1/2 cup of water by mixing it together until it thickens.
  • Blend all bechamel sauce ingredients including cauliflower, in a blender with HALF of the slurry mixture (use more as needed to loosen), and set sauce aside. You'll want the sauce to be thick enough to coat a spoon but still pourable.
  • Make a quick topping to set aside: mix 2 Tbsp nutritional yeast with 1-2 tsp of cinnamon, and a pinch of sea salt in a bowl. Keep for the very end!

Put it all together!

  • To your greased baking dish, add two-thirds of your spaghetti squash to the bottom and pack it in a single layer. I patted mine down with a fork to make sure there were no empty pockets.
  • Then, add all of your ground meat on top of that, also packing it in well with a fork in a single layer.
  • Now, pour two-thirds of your bechamel sauce over the meat. With your wooden spoon, lightly push the sauce to cover the meat fully. If at this point you feel more liquid will be needed, add that to the remaining sauce in the blender and blend it on high for 30 seconds. If two-thirds of the sauce covered the meat well and you have one-third left, you’re in good shape and don’t need the remaining liquid.
  • Now, with your hands, pull apart some of the squash to the width of your baking dish. Place the squash “in stripes” so you are controlling the amount of squash and can make sure it’s even but not sinking into the sauce. Make sure you’ve covered it in a single layer.
  • Lastly, add the remaining bechamel sauce over top, lightly pushing with your wooden spoon again to cover the squash. And add your nutritional yeast-cinnamon topping lightly and evenly over the whole dish. 
  • Bake for 40 minutes until the top is golden-brown and bubbling on the edges. Let rest for 5-10 minutes before cutting into it. Enjoy! This will keep well in the fridge for a week.


Diet: Greek
Course: Main Course

Oh and hayyy, do you love my enamel baking dish and forks? I just got them, courtesy of Amara.com!

Paleo Spaghetti Squash Pastitsio (Greek Baked Ziti w/ Dairy-free Bechamel) dairy-free, gluten-free, grain-free, low-carb, AIP-friendly via Food by Mars
-Alison Marras
This post may contain affiliate links. Please read my disclosure policy.

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  1. Hi, I noticed that you list olive oil as an ingredient in the ground meat layer but in the instructions you say to add ghee/lard to the pan and not olive oil.

  2. Allergies are frustrating. Thanks for saving me time, money and heartache changing recipes. Dairy free, gluten free…among others

  3. This is my new family favorite for meal prep and as a Greek… I APPROVE! I’m so happy we can have a dairy-free version of my beloved pastitsio- thank you!!♥️

  4. This is amazing. I’m making it for the second time and this time I don’t have fresh cauliflower in hand. Can I use frozen cauli rice in place. If so any cha he’s to recipe? Thank you!!

  5. This is really good. I cannot use nutritional yeast, so I used an AIP “Mozzarella” that I made last night, both in the sauce, and a little chopped up and spread on top. Thank you for this recipe, it will definitely be a regular meal.

  6. What can be used to substitute coconut cream? We have trouble digesting such a fatty ingredient. Thank you!

  7. This looks awesome…but sadly (cry for me?) it’s nearly impossible to find spaghetti squash in my area (northeast England.) I can get cans of hearts of palm pasta..do you think it might work? No cassava pasta here either, unfortunately! 

  8. What a delicious looking meal. Love bechamel sauce. This looks fantastic. Trying this soon. Thaanks for sharing

  9. Whoa! That beschamel is beyond amazing, I like it better than the milk/flour based ones I’ve had. Will make again! I think I messed up a little by using an 8×8 glass dish, it made it too thick and I think l it let the squash take over. Next time I’ll use a more rectangular dish and perhaps more meat and a little less squash. Recipe was so delicious! Thank for for posting this.

  10. I just discovered this recipe and it is AMAZING!!! I make at least once every couple of weeks. The Bechmel sauce is sooooo good. I’ve even contemplated making a batch and drinking it straight from the blender. Thank you for coming up with such a fantastic recipe! 

    • Why thank you so much, Diane!! I’m excited you enjoyed it! Perhaps you didn’t realize it, but you rated the recipe with 1-star but seemed to love it, was that intentional? Please let me know if I can help at all!

  11. This is AMAZING! One of my husband’s favorite’s!  I use the whole can of coconut cream. I also use a pound of ground beef.

  12. Hi Alison!  Thrilled to find your site – I may have missed it, but what are the directions for doing the squash in the Instant Pot?

  13. Being at home now with the quarantine I have lots of time to find good healthy recipes and cook! I made this for dinner tonight and it was fantastic! It tasted as if I had mashed potatoes as the crust. Thank you!

    • so glad you’re enjoying cooking at home! it’s definitely a silver lining 🙂 love that you enjoyed this recipe!!

  14. My husband and I spent the past three Christmases in Greece, so we were feeling nostalgic back in the States this year. This Christmas was also my first with my Hashimoto’s diagnosis. I was so SO happy to find this recipe — it was the perfect Christmas dinner for us. Every bite transported us to our favorite Cretan restaurant. Thank you so much. Any chance you’ve figured out a Hashimoto’s-friendly version of vasilopita? 🙂 

  15. I tried it…sent to my sis who also tried and we all LOVED it! I am going to give this a try – what do you think: Next time I am going to mix the meat layer WITH the squash layer on the bottom (to give it a little more OOMPH)…and maybe add 3 beaten eggs in one for anyone who does eat eggs (to give it that stiffer pasta feel). I will let you know if it works!

    • Hi Michele!
      I’m so glad you’ve all been enjoying it – thanks so much for sharing! Your ideas sound delicious… anytime we can add more OOMPH, I AM DOWN. haha – What’s funny is I had to tie my hands using eggs in this so I could make it Autoimmune Paleo Friendly.. but my instinct was to add an egg to either the bottom to make it stiffer OR to add yolk in the bechamel even. I was so impressed that I didn’t actually need it at all, but for those who tolerate eggs, it can only be a benefit to the texture and taste (and of course added protein). So you’re thinking the same! I think it could definitely have that effect since I often make frittatas with sp. squash as the “crust” and the egg seeps into it making it stiff. Let me know how it turns out!! XO

    • I didn’t freeze the whole dish, since we finished it, but I froze a cup of the sauce to see how it freezes and thaws. Tonight I put the thawed leftover sauce on some cabbage rolls before baking them and it was perfect! I also made the sauce for “regular” GF lasagna and pizza last week and both were a hit.

  16. I have more of a question… This recipe sounds incredibly awesome.. but I hate coconut. What could I substitute for the coconut cream? Thanks!

    • Hi Tiana!
      I went with the coconut since I could easily cover up the flavor with the nutritional yeast, lemon and the cauliflower mellows it out – so if it helps at all, you won’t taste the coconut at all. If you need a sub, I don’t think it will taste the same, but you can sub cashew “cream” instead if you’re eating nuts (soak cashews overnight, drain and blend – use the same amount as the coconut cream). For other nut-free options, you can try searching for a cauliflower cheese recipe! XO

  17. Is this weight watcher smart point friendly? Do you have the nutritional information so that I can plug it into the WW app please?

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