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Baked Stuffed Tomatoes with Spinach and Cottage Cheese

I can’t wait for you to try this baked stuffed tomatoes recipe! Full of flavor from a decadent cheesy spinach filling and baked until golden and bubbly, this Italian-inspired dish makes an excellent appetizer, side dish, or high-protein meatless main course, packing an impressive 20 grams of protein per tomato! 

four spinach and cheese baked tomatoes with a cutting board behind them with a block of cheese, microplane, herbs, and pepper mill

Whether you’re blessed with a bountiful tomato harvest or just looking for a high-protein vegetarian dish, look no further than these baked stuffed tomatoes. This easy recipe is a testament to the joys of healthy homemade cooking –and personally, one of my favorite ways to savor those big, juicy summer ‘maters!

It couldn’t be any easier! Simply scoop out the tomato innards, fill each one with a flavorful blend of cottage cheese, Parmesan, savory seasonings, and spinach, and pop them in the oven. In under 30 minutes, you’ll have a batch of THE BEST stuffed tomatoes!

I’ve served these tomatoes as a unique side dish with grilled chicken skewers, salmon, and steaks. They also make an excellent appetizer for elegant occasions and holiday gatherings. And let’s not forget their potential as a high-protein vegetarian meal.

Why you’ll love this recipe

  • Easy-peasy. Achieve a flavorful dish with minimum fuss.
  • Serve it your way. Whether you’re looking for a standout side dish, a crowd-pleasing appetizer, or a satisfying meatless main, these stuffed tomatoes are up for the challenge.
  • Vegetarian-friendly. It’s the perfect protein-packed meatless meal.
  • Gluten-free & low carb. This dish has no gluten or grains, catering to certain dietary preferences without skimping on satisfaction. 
  • Customizable. Feel free to mix and match fillings and seasonings to your heart’s content. 

Ingredients you’ll need

ingredients for stuffed tomatoes measured out on a counter
  • Tomatoes. I prefer large beefsteak tomatoes, but you can use any medium to large variety with firm, slightly thicker skin, such as heirloom, or Big Boy tomatoes. Select ones that are ripe but firm with smooth, unblemished skin. 
  • Coarse salt. Used for extracting excess moisture from the tomatoes and seasoning. 
  • Extra virgin olive oil. To sauté the filling veggies and drizzle on the tomatoes before baking. 
  • Onion. Adds sweetness and depth to the filling. I used sweet Vidalia onion, but white or yellow onion also works. 
  • Garlic clove. Infuses the filling with aromatic-savory flavor.
  • Frozen spinach. Provides a convenient way to sneak greens into the dish. Thaw, drain, and squeeze the spinach completely dry before adding it to the filling.
  • Cottage cheese. Adds creaminess and protein to the filling. Depending on your dietary preferences, opt for a low-fat or full-fat small curd variety.
  • Parmesan. Adds a rich and nutty flavor to the filling mixture and melts beautifully on top. Grate the cheese directly from a block for better blending and melting. 
  • Egg yolks. Helps bind the filling ingredients and adds richness. 
  • Basil. Imparts an aromatic herbaceous flavor. I used ½ teaspoon dried basil, but you can use 1-2 teaspoons of fresh basil if preferred. 
  • Salt and pepper. To taste. 

How to make baked stuffed tomatoes

Step 1: Hollow out the tomatoes. Wash and dry the tomatoes. Using a paring knife, slice off the tops and carefully scoop out the seeds and pulp with a spoon from each tomato, careful not to pierce the sides.

how to score a tomato to hollow it out
tomatoes sliced in half with the center hollowed out

Step 2: Drain excess moisture. Sprinkle salt inside each tomato, and place them cavity-side down on paper towels to drain.

tomatoes sprinkled with salt and turned upside down to drain on paper towels

Step 3: Sauté the vegetables. Meanwhile, heat olive oil in a large skillet and sauté the onion until translucent. Add the garlic and drained spinach, cover, and cook on low heat for 8-10 minutes, stirring occasionally. 

sauteed spinach and garlic in a skillet

Step 4: Prepare the filling. Combine the cottage cheese, parmesan cheese, egg yolks, basil, salt, and pepper in a large bowl. Add the spinach mixture and mix well. 

filling for stuffed tomatoes in a bowl

Step 5: Stuff the tomatoes. Pat the cavities dry, then place the tomatoes in a greased baking dish. Fill each cavity with the spinach mixture and spray or drizzle with olive oil (I do both). 

four tomatoes in a square baking dish stuffed with spinach and cheese filling

Step 6: Bake the tomatoes. Transfer to the 350℉ preheated oven and bake until the filling is bubbly. 

Step 7: Melt the cheese on top. Finely grate extra parmesan cheese on top of each tomato, and continue baking until the cheese is golden and melted. 

Step 8: Garnish and serve. If desired, sprinkle a pinch of salt and freshly chopped basil or parsley over each tomato, and enjoy!

spinach and cottage cheese stuffed tomatoes with melted parmesan on top fresh from the oven in a baking dish

Recipe tips

  • Drain the tomatoes. It is imperative to place the hollowed-out tomatoes upside down on paper towels for at least 30 minutes before proceeding with the recipe! This critical step helps drain excess moisture, preventing the filling from becoming watery during baking.
  • Drying the spinach. Soggy spinach can also be the culprit behind a watery filling. You must thaw it completely, then wrap it in a clean kitchen towel or paper towel and squeeze out as much moisture as possible before using it. 
  • Avoid overseasoning. Remember that the cheeses will provide decent saltiness, so I highly recommend going easy on the salt until you’ve tasted the filling mixture. 

Variations

  • Vegan stuffed tomatoes – Substitute dairy-free alternatives for the cottage cheese and Parmesan, such as soft tofu or vegan cream cheese for creaminess and nutritional yeast for the cheesy flavor.
  • Incorporate grains – Mix cooked grains, like quinoa, rice, bulgur, or couscous, into the filling before stuffing the tomatoes. For low-carb stuffed tomatoes, consider cooked cauliflower rice. 
  • Vegetable add-ins – Mix and match the spinach with other veggies like diced bell peppers, mushrooms, zucchini, or chopped artichoke hearts. Sauté the veggies with the onion and garlic before incorporating them into the filling.
  • Alternate cheeses – Experiment with different cheeses in the filling, such as feta, goat cheese, mozzarella, fontina, gruyère, Swiss, or brie. Just be mindful of the melting properties of the cheese you choose.
  • Make it meaty – Add ground meat like sausage, beef, or turkey for a high-protein twist. Brown the meat separately before combining it with the other filling ingredients.
  • Switch up the seasonings – In addition to basil, add herbs like thyme, oregano, or parsley for extra flavor. Consider Spices like paprika, cayenne pepper, or red pepper flakes for a kick of heat.

Storing & freezing

Storing: Place leftover baked stuffed tomatoes in an airtight container and keep refrigerated for 2-3 days. 

Freezing: Arrange the cooked and cooled stuffed tomatoes in a single layer on a parchment-lined baking sheet and place in the freezer. Once frozen, transfer the tomatoes to a freezer-safe container and keep them frozen for 2-3 months. Thaw overnight in the fridge before reheating. 

FAQ

How long do you bake stuffed tomatoes?

Stuffed tomatoes typically take around 25-30 minutes to bake at 350°F. However, the exact baking time may vary depending on the size and ripeness of your tomatoes and the filling ingredients used. They’re done when the tomatoes are tender, and the filling is golden brown and bubbling.

Can I substitute fresh spinach in the filling mixture?

Yes, you can use fresh spinach instead of frozen spinach but don’t just toss raw spinach into the filling mixture. You must cook it until it’s wilted and allow it to cool slightly before adding it to the filling.

Can I make this in the air fryer?

Yup! Preheat your air fryer to 350°F, arrange the stuffed tomatoes in a single layer in the basket, and cook for about 15-20 minutes or until the tomatoes are tender and the filling is hot and bubbly. Check periodically to avoid overcooking.

Are stuffed tomatoes good to make ahead?

Absolutely! You can prepare the filling mixture, hollow out the tomatoes, and then store them separately in the refrigerator overnight until you’re ready to bake. For the best results, assemble the stuffed tomatoes just before baking.

More stuffed vegetable recipes

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zoomed in photo of a baked tomato with a bubbly spinach and cheese filling
close up of a stuffed tomato in a baking dish with melted parm on top

Baked Stuffed Tomatoes with Spinach and Cottage Cheese

An Italian-inspired recipe for baked tomatoes stuffed with a blend of spices, parmesan cheese, cottage cheese, and spinach. High in protein and delicious!
5 from 2 votes
Print Pin Rate
Course: Main Course, Side Dish
Cuisine: Italian
Prep Time: 30 minutes
Cook Time: 30 minutes
Total Time: 1 hour
Servings: 4
Calories: 254kcal
Author: Amee

Equipment

  • square baking dish

Ingredients

  • 2 tbsp extra virgin olive oil
  • 4 large ripe red tomatoes beefsteak or other large tomato variety
  • salt for draining tomatoes
  • ½ medium onion finely diced- I use Vidalia but white or yellow onion works here too
  • 1 large garlic clove minced
  • 12 oz frozen spinach thawed, drained, and completely squeezed dry
  • cup 2% cottage cheese small curd
  • ½ cup shredded parmesan cheese
  • 2 large egg yolks
  • 1 tsp salt
  • ½ tsp black pepper
  • ½ tsp dried basil you can also use 1-2 tsp of finely chopped fresh basil
  • olive oil cooking spray
  • block of parmesan or pecorino romano for grating on top
  • optional garnishes: chopped fresh basil or parsley

Instructions

  • Wash the tomatoes and pat dry. Slice the top off and hollow out the inside of the tomato, being careful not to pierce the sides. I use a small paring knife for this, running it around the inside and scoring it into 4 sections to remove. Carefully scoop out the cavity with a large spoon, removing the seeds and membrane.
  • Salt the cavities and place them upside down on paper towels to drain for 30 minutes.
  • Preheat the oven to 350 degrees F. While the tomatoes are draining, prepare the filling.
  • Heat the olive oil in a large skillet over medium heat. Saute the onion until translucent, about 3-4 minutes.
  • Add the garlic and drained spinach to the skillet, cover, and cook on low heat for 8-10 minutes, stirring occasionally.
  • In a large bowl, stir together the cottage cheese, parmesan cheese, egg yolks, salt, pepper, and basil until combined.
  • Add the spinach mixture to the bowl and stir the filling well to mix.
  • Pat the tomato cavities dry with paper towels and place them into a greased square baking dish. Spoon the spinach mixture into the tomatoes. Spray with olive oil spray (or drizzle with olive oil- I do both) and bake for 25 minutes.
  • Using a microplane grater, finely grate some extra parmesan cheese on top of each tomato and bake for 5-7 minutes more, until th cheese is melted and tomatoes are bubbly.
  • Garnish with coarse salt and freshly chopped parsley or basil, if desired.

Notes

  • Drain the tomatoes. It is imperative to place the hollowed-out tomatoes upside down on paper towels for at least 30 minutes before proceeding with the recipe! This critical step helps drain excess moisture, preventing the filling from becoming watery during baking.
  • Drying the spinach. Soggy spinach can also be the culprit behind a watery filling. You must thaw it completely, then wrap it in a clean kitchen towel or paper towel and squeeze out as much moisture as possible before using it.  

Nutrition

Calories: 254kcal | Carbohydrates: 15g | Protein: 20g | Fat: 14g | Saturated Fat: 4g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 7g | Cholesterol: 103mg | Sodium: 1145mg | Potassium: 837mg | Fiber: 5g | Sugar: 8g | Vitamin A: 11741IU | Vitamin C: 31mg | Calcium: 339mg | Iron: 3mg
Tried this recipe?Mention @ameecooks or tag #ameecooks!
Amee Livingston
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4 Comments

  1. This looks very tasty. I have a bumper crop of tomatoes right now and I’m looking for a new way to use them. I’ll give this a try. Thanks!

  2. 5 stars
    Very delicious, only had two extra large tomatoes placed remainder of stuffing in corner of baking dish. I cook for my 85yo mother it’s a great way to get in protein for her. Website would not let me give five stars but I give it five stars. Thank you Amee!

    1. Hi Mary! That’s so weird, I’ll have to check on why the star rating isn’t working properly, but I can fix that for you. 🙂 Thank you so much for the review and I’m so thrilled that you enjoyed them!

5 from 2 votes (1 rating without comment)

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