Baked Eggs in Spaghetti Squash Nests

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A muffin tin with a nest of spaghetti squash and a baked egg in each tin
You’re going to LOVE these baked eggs, baked in a nest of spaghetti squash which has a flavor similar to hash browns. Perfect for breakfast or brunch, and because I love my eggs with sriracha, I top mine with a few dashes just for an extra kick, totally optional of course.
Delicious Baked Eggs in Spaghetti Squash Nests

This recipe calls for cooked spaghetti squash. There’s a few ways to cook it, you can either roast in the oven cut side down in a baking dish at 375°F for 1 hour, or the quicker way is to pierce it all over with a fork, then microwave until the skin is soft, about 2 to 3 minutes per pound. Remove the seeds and scrape the strands with a fork. Because I had the time, I did this in the oven, the method I prefer.

Two roasted halves of spaghetti squash
A muffin pan lined with spaghetti squash mixture and a raw egg on top of each
A muffin pan with spaghetti squash mixture and a baked egg in each tin

You're going to LOVE these baked eggs, baked in a nest of spaghetti squash which has a flavor similar to hash browns. Perfect for breakfast or brunch, and because I love my eggs with sriracha, I top mine with a few dashes just for an extra kick, totally optional of course.
Print WW Personal Points
3.5 from 6 votes
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Baked Eggs in Spaghetti Squash Nests

152 Cals 10 Protein 10 Carbs 8 Fats
Total Time: 45 mins
Yield: 6 servings
COURSE: Breakfast, Brunch
CUISINE: American
You're going to LOVE these baked eggs, baked in a nest of spaghetti squash which has a flavor similar to hash browns. Perfect for breakfast or brunch, and because I love my eggs with sriracha, I top mine with a few dashes just for an extra kick, totally optional of course.


  • cooking spray
  • 1 1/2 cups cooked spaghetti squash, from 1 medium
  • 1 small onion, minced
  • 1 large egg white
  • 1 tbsp butter
  • 2 tbsp dried parsley
  • 1 tsp garlic powder
  • 1 tsp kosher salt
  • 1/8 tsp black pepper
  • 1/4 cup all purpose flour, or GF King Arthur flour
  • 1/3 cup shredded Pecorino Romano cheese
  • 6 large eggs


  • Preheat the oven to 425°F. Spray a muffin tin with oil.
  • Place the cooked spaghetti squash in a bowl.
  • In a medium skillet, saute onions in butter on medium-low heat for about 5 minutes, or until soft.
  • Add this to the bowl with the spaghetti squash along with the egg white, parsley, garlic powder, salt, pepper, flour and cheese and mix well.
  • Scoop 1/4 cup into each tin, pressing up the side to create a nest.
  • Bake 18 to 20 minutes, until the edges become golden and crisp.
  • Reduce the heat to 375°F.  Remove from oven and carefully crack 1 egg into each tin.
  • Bake an additional 10-12 minutes, or longer depending on how you like your eggs.


Serving: 1nest, Calories: 152kcal, Carbohydrates: 10g, Protein: 10g, Fat: 8g, Cholesterol: 194mg, Sodium: 352mg, Fiber: 1g, Sugar: 1g
WW Points Plus: 4
Keywords: Gluten Free, low carb, Vegetarian Meals

A mixing bowl with cooked spaghetti squash, diced onion, grated Pecorino Romano cheese, and dried herbs
A muffin pan with spaghetti squash in each tin
A muffin tin with spaghetti squash mixture and topped with a raw egg in each tin

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  1. I absolutely love the flavor of the spaghetti squash in this recipe.  However I only like my eggs with a very runny yoke but no goo, and when I bake eggs in the oven I always find the yoke is too done for me.  So this time I spread the spaghetti squash mix out on a cookie sheet and baked it to an almost crispy texture.  Then I divided it up into flat portions.  I heated it up in a small pan, cooked a couple of basted eggs the way I like them and put them on top of the squash.  PERFECT! 

  2. I have read on here that a lot of people have tried this recipe and it was a fail because the squash was too mushy. What worked for me is to after roasting the squash and letting it cool, I spread the squash over a kitchen towel and then squeezed out as much as the water as possible. Doing that along with adding the flour should result in a crisper cup. Also—I greased my tins pretty well and used olive oil rather than just a spray. Mine turned out really tasty and the right texture. Hope this helps! 

  3. I have absolutely loved every recipe I have ever tried from Skinnytaste…except these. These were a total fail on all levels…mushy mess, burnt on the sides of my pan. I’m literally throwing my muffin pan away because it will take me a week to scrub these out. I’m so disappointed. Idk what went wrong but I will not be trying this project again.

  4. I fell in love with these last fall when I had an overabundance of spaghetti squash and was looking for something new. I made these often until my squash was gone. Now that the squash is back in season, the first thing I’m making with my squash is these egg cups! I think this time I’ll have to make double batches because my husband and I go through one batch too quickly, including having to eat one immediately after taking out of the oven!

  5. Huge miss- do not make.
    Wasted 6 organic eggs and beautifully roasted spaghetti squash- followed recipe exactly, the “batter” was just mush, no matter how long it baked! Didn’t want to give guests salmonella so I had to throw it all away.

  6. Just made this and OMG, so yummy!!!! I didn’t have dried parsley so I subbed half Italian seasoning and half dried basil. These are delicious and filling for only 2 points!

  7. I had a spaghetti squash to use, and a had all of these ingredients in my house.  THEY ARE SOOOOO GOOD!    The real test will come when I try to reheat 

  8. Wondering if I could make these without flour. Could I omit it? Or could I use almond flour or cassava flour? Or something else? If so, how much?

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  10. Love this! I tweaked it a little though. I doubled the spaghetti squash, used less and light butter and baked in a bigger muffin to make 6 spaghetti squash “hashbrowns” (for 1 pt each) then just cooked my egg on the stove. Delicious!! Thanks for your great recipes.

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  12. These were a fail for me 🙁 I baked the spaghetti squash cups about 3x the time given and they never came together or got crispy. 

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  14. Making these now. I made spaghetti squash primavera the other day, now using the leftover squash for these. Now I need to stop salivating and wait for them to be done. ????

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  16. For make ahead…I'm thinking make the nests, then stop. Remove from pan and refrigerate, then cook eggs in nests as needed. They might even freeze ok this way. What do you think?

  17. My spaghetti squash always gets super watery….what am I doing wrong? I roast it just like your directions with the cut side down.

  18. Thanks, Gina, for your wonderful recipes! You've made cooking light fun again. When making this for Sunday brunch, I packed the squash mixture into 4 to 6 oz. sprayed custard cups or ramekins–no mess, no spillovers, and a nice crust all around the nests. Reduced baking time for both the nests and the eggs by 2 or 3 minutes, but my stove runs hot. My diet-conscious guests loved it! Will make again adding minced red bell pepper and some turkey bacon crumbles for a Potatoes O'Brien-style dish. Thanks for a memorable meal!

  19. I am always looking for interesting breakfast/brunch items to make when we have overnight guests. I made spaghetti squash the other night and saved half of the roasted squash to use to make this recipe. I was able to get the 1.5 cups required from just half of the squash, which surprised me.
    Although I thought the little egg nests were clever, I found the recipe to be a bit labor intensive for my purpose. When I have guests, I prefer to have something I can pretty much make ahead so I can spend time with my guts rather than cooking. I suppose you could make the nest mixture ahead, then just do the baking the morning of.
    Getting the nests out neatly was a challenge, too, because the bottoms were still not crisp. They tasted salty, which was surprising.
    To help avoid the messiness some folks mentioned, I cracked the eggs into a cup first, making it easier to pour them into the prepared nests. That said, I still had some spillover. I used a standard muffin tin and large (not jumbo) eggs. Fortunately, the muffin pan was nonstick, plus I'd sprayed the tin as directed, so it was easy to clean up.

  20. Just made these for lunch and OMG they are soooo delicious! I have a stupid question. I am not a cook, but I make a TON of your recipes! Mine turned out pretty mushy and soggy, not crunchy at all. I am pretty sure I had too much squash since mine was HUGE. I made 9 instead of 6 to try to make up for it, and I even pulled out a lot of the squash. To measure out 1.5 cups, I put the cooked squash in a measuring cup. My question is whether or not that is the correct way to measure out a cup and a half of squash, and also whether based on the info you have any clue what I did wrong. PS: they were freaking delicious even mushy so I can't imagine how good they would be with some crunch! Thanks!

    • Yes that is the correct way to measure the squash. The texture should be slightly crunchy on top, but the bottom will be more like a mashed potato.

  21. It's been asked a few times but not answered… how well do these freeze?

  22. Fantastic! I made it like a casserole.

  23. Yum! Btw, LOVE the muffin pan!

  24. Very clever indeed, looks like little nests!

  25. I love these. They are so tasty and super healthy!! I love the trick of making the spaghetti squash in the microwave!! Saved so much time on Meatless Monday last week! I had enough squash leftover to do them again on Easter. My husband even liked them despite the squash! I did have a bit of an overflow problem with the eggs as well. I tried to crack them and get the yolks in without all of the white. This helped some, but a tad less squash would probably help.

  26. Holy crap. Cutest muffin pan ever.

  27. I added a little cayenne to the spaghetti squash mixture, and it tasted great. However, I made an enormous mess when cracking the eggs on top. Did anyone else have an overflow issue? I might make seven instead of six next time.

    • Yep – big mess over here too! I'm guessing that super-cute muffin tin has larger sized cups than a regular tin. This one goes under the "Pinterest Fails" category for me!

  28. The house smells lovely waiting for these little cups of happiness to finish cooking. Can't wait to try them. And I just happened to have a spaghetti squash in the frig! I will say that next time I may be either using a large muffin tin or small eggs. Had some spill over out of the cups, even after pressing them again. Can't wait to see how these turn out.

  29. This sounds amazing. I often pin things from this site, but I'm pretty sure I'm actually going to make this one!

  30. This looks and sounds fantastic! Loving the idea of little spaghetti nests with egg in them, delicious 😀 x

  31. I made these last night and refrigerated them for my breakfast this week! This morning I popped one in the microwave for about 30-45 seconds and it was super yummy!

    The only problem I had was that the squash was a bit soggy at the bottom. I think I may have added a bit too much squash. Since I wasn't eating these right away I whisked the eggs together before I added them to the nests which worked perfectly. I will definitely be making these again, just a bit less squash. The flavor was great! Another fantastic Skinnytaste recipe!

    • Thanks so much and yes you are probably right..squash probably made them a little soggy. But I'm glad you liked it.

  32. This looks so delicious and healthy! And that muffin pan….Gorgeous!!!

  33. The sodium comes from the cheese.

    • I thought that also, and the highest sodium content I found online for Pecorino Romano cheese was 135mg for 1T. (I did the math, 1/3 cup = 5T + 1tsp, 3 tsp = 1T, so it's 720mg sodium from cheese for the ENTIRE recipe, spread over 6 servings = 120mg.) So, 1 egg on top 70mg + 120mg from cheese + the sodium spread over 6 servings from the egg white and squash (which is negligible amount, about 16mg per), so I get 206mg before the added salt. It's OK… I was just trying to understand the sodium content because it seemed VERY HIGH.

  34. Gina, how did you come up with 352mg of sodium (without salt)? This seems high I looked up spaghetti squash & 1 cup has 17mg, 1 large egg 70mg, flour 0mg…it's not adding up. I'm not seeing where the additional sodium comes from.

  35. What a great idea and the perfect balance of carbs, protein and fat! Can't wait to try this!!! #focusedonfit

  36. Do these store well in the refrigerator?

  37. I was wondering if you could do this with scrambled eggs and add bacon or ham bits, almost like an omlet instead of a baked egg.

  38. Once cooked, did these come out of the muffin pan easily? Any suggestions on how to get them out without messing them up?

    • I haven't tried it…bit it does recommend using cooking spray. Also let cool for a few minutes in the pan to let it set and use a butter knife to go around the edge of each cup in and up & down motion. That always does the trick with regular muffins for me.

  39. I was wondering if just the cups would freeze okay so I could cook one or two at a time…..

  40. Would these freeze and reheat okay?

  41. Trying it right now!

  42. Great idea to substitute a pastry base for a crunchy squash base

  43. Are you using standard size muffin cups or large?

  44. What a fun spring brunch recipe! That spaghetti squash nest looks delicious!

  45. I definitely need to try spaghetti squash in the microwave!! I always bake it which is great but takes a long time! These little cups look great!

  46. Can you freeze or make ahead and assemble in the morning?

  47. Cut side down so skin is facing up?

  48. Love the little tin.I saw similar at Anthro?
    And HomeGoods….Adorable!

  49. These look so delicious! Perfect for Easter 😀

  50. I LOVE your muffin pan! Where did you get it? And your recipe looks fabulous 😉