Spaghetti Squash Tuna Noodle Casserole Boats

A healthy spin on a comfort food classic, these spaghetti squash tuna noodle casserole boats are filled with loads of creamy goodness and ample protein. Gluten-free, dairy-free, low-carb and paleo! I received free samples and compensation by Genova in exchange for recipe development. All opinions are my own.

Spaghetti squash tuna noodle casserole boats // gluten-free, dairy-free, low-carb and paleo!

Healthy Tuna Noodle Casserole

I remember loving tuna noodle casserole as a kid, but I honestly haven’t had it in years. It makes sense considering tuna noodle casserole isn’t really known for being a health-focused meal. It’s more of a comfort food classic.

Anyhow, given the popularity of my spaghetti squash lasagna boats from last year I thought it would be fun to do a similar spaghetti squash boat recipe with tuna casserole. I’m so glad I had the idea, because this combo is so comforting and delicious. Maria and I both loved the recipe while testing it and Isaac was impressed when I served it up for dinner one night as well.

You can’t go wrong with creamy, noddle goodness… even if the noodles are a veggie!

A healthy spin on a comfort food classic, these spaghetti squash tuna noodle casserole boats are filled with loads of creamy noodle goodness. Gluten-free, dairy-free, low-carb and paleo!

I’m diggin’ this recipe for a bunch of different reasons. 1.) The casserole is served out of a spaghetti squash bowl, which is super fun and meals less dishes. LOVE! 2.) It’s super healthy — loaded with good for you ingredients, protein and healthy fats. 3.) The creamy mushroom sauce is completely dairy-free… made with coconut milk!!

While making the sauce, Maria and I couldn’t help but realize that it’d make a great soup on it’s own so we’ll likely be experimenting with a full blown mushroom soup recipe soon.

A healthy spin on a comfort food classic, these spaghetti squash tuna noodle casserole boats are filled with loads of creamy noodle goodness. Gluten-free, dairy-free, low-carb and paleo!Genova Tuna

For the tuna we used two cans of Genova’s easy open albacore tuna packed in olive oil. Genova’s tuna tastes great, plus it’s wild-caught, non-gmo and Marine Stewardship Council (MSC) certified, which means the fish are responsibly caught by a certified sustainable fishery. Learn more about their new cans with the blue label and the MSC certification here.

A healthy spin on a comfort food classic, these spaghetti squash tuna noodle casserole boats are filled with loads of creamy noodle goodness. Gluten-free, dairy-free, low-carb and paleo!

For the topping we used gluten-free sprouted seed crackers, but you could also use almond flour crackers or another cracker you love. Store bought or homemade crackers will work. You certainly don’t need the crackers, but they add a nice crunch and a bit of texture to an otherwise soft and creamy dish.

A healthy spin on a comfort food classic, these spaghetti squash tuna noodle casserole boats are filled with loads of creamy noodle goodness. Gluten-free, dairy-free, low-carb and paleo!

If you make this spaghetti squash tuna casserole please be sure to leave a comment and star rating below letting me know how it turns out. Your feedback is super helpful for the EBF team and other EBF readers. 

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Two spaghetti squash tuna casserole boats on white plates.

Spaghetti Squash Tuna Casserole

  • Author: Brittany Mullins
  • Prep Time: 15 minutes
  • Cook Time: 60 minutes
  • Total Time: 1 hour 15 minutes
  • Yield: 4


A healthy spin on a comfort food classic, these spaghetti squash tuna noodle casserole boats are filled with loads of creamy goodness and ample protein. Gluten-free, dairy-free, low-carb and paleo!


  • 2 5 oz Easy Open Cans Genova Albacore Tuna in Olive Oil, drained
  • 1 tablespoon olive oil
  • 1 15 oz can coconut milk (regular or lite)
  • 1 large yellow onion, chopped
  • 2 cloves garlic, minced
  • 2 cups sliced baby bella mushrooms
  • 1 1/2 teaspoon pepper
  • 1 1/2 teaspoon sea salt
  • 1 medium-large spaghetti squash
  • 1 cup frozen peas, thawed
  • 1/4 teaspoon cayenne pepper
  • pinch of nutmeg
  • 1/2 cup crushed sprouted seed or almond flour crackers
  • parsley, for garnish


  1. Heat oven to 350°. Chop spaghetti squash in half length wise, scoop out seeds with a spoon. Coat the inside of each half with a tiny bit of olive oil. Place on a baking sheet, cut side down and bake for about 40-50 minutes or until you can easily pierce a fork through the squash.
  2. While squash is baking, prepare your sauce by adding oil to a medium pot on medium-high heat. Add onion, garlic, salt, pepper, cayenne and nutmeg. Cook, stirring often, for about 10 minutes or until onion and garlic are aromatic and translucent.
  3. Add mushrooms and cook until onions are browning a bit and mushrooms are soft.
  4. Add in coconut milk and cook on medium high until sauce has reduced in half, to the thickness of gravy. Be sure to stir the sauce often so that it doesn’t stick. This should take about 15-20 minutes. Once reduced, remove sauce from heat, add in thawed frozen peas and tuna. Stir to combine.
  5. By this time your squash should be fully cooked, or close to it. Remove squash from oven and let cool for 5-10 minutes before scraping the inside of the squash with a fork to remove the spaghetti-like strands.
  6. The cooked spaghetti squash may seem liquidy. If so, place in a fine-mesh colander to remove access liquid. Press strands down with a fork or spatula to really press it all out.
  7. Add drained spaghetti squash strands into the sauce mixture and toss to combine.
  8. Spoon spaghetti squash tuna mixture into the bottom of each squash half. Top each with 1/4 cup cracker crumbs.
  9. Bump oven temp to 375° and bake for 10 minutes, or until casserole is heated through and crackers are a little golden.
  10. Remove from oven, sprinkle with fresh parsley and enjoy!
  • Category: Lunch/Dinner
  • Method: Bake
  • Cuisine: American


  • Serving Size: 1/4 of recipe
  • Calories: 391
  • Sugar: 7g
  • Fat: 25g
  • Carbohydrates: 22g
  • Fiber: 5g
  • Protein: 22g

Keywords: spaghetti squash tuna casserole

My Favorite Way to Cook Spaghetti Squash

If you’re not making spaghetti squash boats, my favorite method of cooking spaghetti squash involves slicing it into rings and roasting it. It results in long spaghetti-like noodles and squash that isn’t watery! Check out my how guide for how to cook spaghetti squash.

More Spaghetti Squash Recipes to Try:

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Recipe rating

    1. Lily
      February 2, 2021 AT 9:44 pm

      My husband was not very excited about this meal so I kept putting it off. Eventually, I needed to use the squash so I made this dish tonight and as expected- he went for seconds! It’s all the benefits of comfort food without the high calories. He said it felt very nostalgic. I will be making the lasagna version this weekend when my mom visits!

      1. Brittany Mullins
        February 3, 2021 AT 10:13 am

        Ahh yay, I love hearing that!! So glad it was a hit!! So glad you finally got to make it and thanks for coming back to leave a review. I so appreciate it!

    2. Tracy
      January 18, 2021 AT 7:45 pm

      I don’t normally leave comments, but this recipe was so delicious, I had to leave a comment! I actually made this like a traditional casserole and used gluten free crackers for the top. The taste is incredible!

      1. Brittany Mullins
        January 20, 2021 AT 12:17 pm

        Ahh yay!! That makes me so happy to hear. I’m so glad this recipe was a hit. Thanks for coming back to leave a review, Tracy. I really appreciate it. 🙂

    3. susan burch
      March 27, 2020 AT 7:18 pm

      I had such high hopes for this recipe after reading the feedback. I followed the recipe exactly, something I do not normally do. I was very disappointed. It was kind of tasteless 🙁 and could barely taste any spice. I have to figure out what to do with what is left. Sorry.

      1. Brittany Mullins
        March 30, 2020 AT 3:25 pm

        Oh no!! I’m so sorry to hear that, Susan. And you didn’t skip or leave out any of the spices? You can always add in more spices based on your taste preference once it’s already cooked.

    4. susan burch
      March 27, 2020 AT 11:11 am

      I just made this. I have not tasted it yet, but, it is grey so not very appetizing looking. I covered it with panko and butter. Will let you know the outcome 🙂

    5. Momof3
      January 23, 2020 AT 11:25 pm

      It was super yummy and creamy and I loved it! But it was too spicy for the rest of the family. Kids couldn’t handle it and my husband doesn’t do spicy. Next time I’d really cut down on the cayenne and pepper.

      1. Brittany Mullins
        January 23, 2020 AT 11:33 pm

        I’m glad you enjoyed this recipe! And yes, you can definitely lower the amount of cayenne / pepper based on your taste preferences. Thanks for coming back to leave a comment + star rating, I appreciate it.

    6. Carrie Hodges
      January 7, 2020 AT 5:02 pm


      1. Brittany Mullins
        January 8, 2020 AT 12:32 pm

        I’m so glad you enjoyed this recipe, Carrie. Thanks for coming back to leave a star rating, I so appreciate it. <3

    7. Anna
      November 29, 2018 AT 6:38 pm

      This recipe is absolutely delicious! I used tuna in water and drained the water and topped with breadcrumbs instead of crackers and a little shredded Parmesan. Super tasty!!

    8. Sonja B
      June 6, 2018 AT 1:54 am

      I made this tonight and we loved it! We didn’t have mushrooms, so I subbed in frozen corn instead. It’s a very versatile recipe because you can sub the veggies and play around with spices and herbs. Our daughter found it to be “spicy” so I’ll reduce the pepper and cayenne next time to reduce heat. This might be a dumb question, but… does it call for one and a half teaspoons (1 1/2 tsp) of sea salt and pepper? Or is it one half of a teaspoon (1/2 tsp) of sea salt and black pepper?
      Thanks for sharing this recipe!

    9. Jen
      April 22, 2018 AT 11:17 pm

      I love your recipe I’ve made it before. I just didn’t have coconut milk on hand so I thought I could substitute it with another milk. I did it with the flour and liquid method instead of soup. It came out good but I still rather have your version.

      1. Brittany Mullins
        April 23, 2018 AT 10:10 am

        Hi Jen! Thanks for letting me know how it turned out. I agree, the coconut milk works best! 🙂

    10. Jen
      March 13, 2018 AT 11:28 am

      Could I use another milk? I’m trying to avoid the store lol

      1. Brittany Mullins
        March 13, 2018 AT 12:22 pm

        hmmm.. I haven’t tried it with any other milk, but you can certainly test it out. I used coconut milk here as a creamy non-dairy sub for canned soup, which is traditional for tuna noodle casserole. Let me know if you test it with another milk.

    11. Frances
      February 26, 2018 AT 8:02 pm

      This was wonderful. I used pouches of low sodium tuna in water and ended up putting all together in a casserole dish. I used shredded steamed carrots instead of peas. We loved this. Can’t believe how much flavor without cheese. The lite coconut milk made a perfect sauce. I even used less of it mixed with veggie broth. This is now my tuna casserole recipe.

    12. Susan
      February 25, 2018 AT 7:41 pm

      I made this recipe tonight. Delicious!! What a great idea for a nice twist on the traditional tuna casserole.

    13. Diane
      January 7, 2018 AT 7:53 pm

      I made this with chicken (and have tuna) also added carrots (cooked in microwave)we love this recipe! I eat low carb and have missed casseroles!

    14. Joanne
      October 19, 2017 AT 6:52 pm

      My daughter made this and it was delicious .im sure I will be making it myself soon.,it was just as good 2 days later. Thanks for the recipe.

      1. Brittany Mullins
        October 22, 2017 AT 4:14 pm

        I’m so glad that you all enjoyed this recipe, Joanne! It’s one of my new favs!!

    15. Hailey Stroup
      October 16, 2017 AT 11:21 am

      This looks yummy!! Do you think it would keep well as leftovers? And, any suggestions on a substitute for mushrooms? Thank you.

      1. Brittany Mullins
        October 16, 2017 AT 11:35 am

        We didn’t have enough leftover for me to test this, but I think it would keep well! You could probably just leave the mushrooms out and use more onions if you don’t like enjoy them. Let me know if you try it. 🙂

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