Delicious & Healthy Vegan Stuffed Tomatoes: A Plant-Based Masterpiece
Transform ordinary tomatoes into an extraordinary and flavorful side dish or a satisfying main course with this incredible vegan stuffed tomatoes recipe. These baked stuffed tomatoes are a symphony of sweet and savory notes, entirely plant-based yet offering a hearty, “meaty,” and surprisingly “cheesy” experience thanks to clever ingredient choices. They are perfect for a quick, healthy weeknight dinner or an elegant addition to any special meal.

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When fresh, ripe tomatoes are in season, it’s a culinary delight! While a simple slice with salt, pepper, and balsamic is always a treat, these **Vegan Stuffed Tomatoes** have quickly become a staple, gracing my table multiple times a week. Their irresistible flavor profile will have you reaching for seconds.
Each juicy tomato is generously filled with a robust quinoa and vegetable stuffing, bursting with umami and baked until perfectly tender. If you’ve yet to discover the joy of baked stuffed tomatoes, prepare for a delightful culinary revelation! This recipe is guaranteed to impress even the most discerning palates.
For those following a dairy-free lifestyle, rejoice! This recipe masterfully achieves a “cheesy” flavor without a hint of parmesan or processed vegan cheese. The secret lies in nutritional yeast, which imparts a savory, umami-rich, and distinctively cheesy taste. It’s a total win, delivering all the satisfaction without the dairy!
Why You’ll Adore These Vegan Stuffed Tomatoes

- Unforgettable Flavor and Satisfaction: These tomatoes are a delightful blend of sweet and savory, with a deeply satisfying umami richness from the mushrooms and a hint of cheesiness from nutritional yeast. Every bite is packed with flavor and hearty texture.
- Allergy-Friendly & Inclusive: Designed to cater to various dietary needs, this recipe is naturally dairy-free, nut-free, vegan, and gluten-free. It’s a fantastic option for families and gatherings where diverse dietary requirements need to be met, ensuring everyone can enjoy a delicious meal.
- Budget-Friendly, Especially Seasonally: When tomatoes are in peak season (typically May through October), they are abundant and affordable. If you’re lucky enough to grow your own, this recipe becomes even more economical, making it a smart choice for delicious, healthy eating.
- Hearty, “Meaty” & “Cheesy” – Yet 100% Vegan: The combination of protein-rich quinoa and earthy mushrooms creates a substantial, almost “meaty” texture that satisfies. Nutritional yeast is the secret ingredient that provides a convincing cheesy flavor, making these stuffed tomatoes feel indulgent without any animal products.
- Ideal for Meal Prep or Effortless Summer Meals: Prepare a batch of the stuffing ahead of time, or even bake the entire dish for easy weeknight dinners. They are fantastic served warm or at room temperature, making them perfect for summer entertaining or quick grab-and-go lunches. Don’t limit them to summer; we enjoy them well into autumn as long as fresh tomatoes are available!
- Versatile for Any Occasion: Whether you need a quick and easy weeknight dinner for your family, an elegant side dish for guests, a delightful brunch item, or a crowd-plepleasing potluck contribution, these stuffed tomatoes fit the bill perfectly.
- The Best Way to Utilize Garden Bounty: If your garden is overflowing with tomatoes of all shapes and sizes, this recipe is your solution. It’s forgiving and adaptable, allowing you to use whatever varieties you have on hand, transforming your harvest into something truly special.
- Excellent as a Light Lunch: Pair one or two of these flavorful stuffed tomatoes with a simple green salad for a wholesome, light, and satisfying midday meal.
Essential Baked Stuffed Tomato Ingredients

- Whole Tomatoes: The star of the show! For the best results, opt for fresh, in-season tomatoes. Larger varieties like beefsteak tomatoes, heirloom tomatoes (if generously sized), or large Roma tomatoes work wonderfully for stuffing. San Marzano tomatoes are often a favorite due to their rich flavor and firm texture. Tomatoes are nutritional powerhouses, boosting the immune system (thanks to Vitamin C and potassium), strengthening bones (with Vitamin K, calcium, and lycopene), and supporting digestive health (due to their fiber and high water content).
- Quinoa: While some recipes use rice, I prefer quinoa for its superior texture and higher protein content, making the stuffing more satisfying and nutritionally dense. Technically, quinoa is a seed rather than a grain, offering a complete protein profile.
- Mushrooms: Shiitake mushrooms lend an incredible “meaty” depth and umami flavor, elevating these to the best stuffed tomatoes you’ll ever taste. Their firm texture holds up beautifully during baking. Portobello or button mushrooms can also be used as alternatives, offering a slightly milder, yet still delicious, flavor.
- Onions: Any sweet white or red onion will add a foundational layer of aromatic flavor to the stuffing. For a subtle twist, you could experiment with thinly sliced leeks, fennel, or green onions.
- Garlic: Fresh garlic is essential for a robust flavor boost. For the best infusion of taste, finely mince the garlic cloves or use a microplane grater. A pro tip: crush or chop your garlic at least 10 minutes before cooking. This allows the allicin (a healthy sulfur compound) to fully develop and oxidize, maximizing both its flavor and health benefits.
- Greens: Chopped kale is an excellent choice as it maintains its texture and nutrients well under the heat of the oven, adding a vibrant color and earthy flavor to the filling. Other hearty greens like collard greens, Swiss chard, or even spinach (though it will wilt down significantly) can be used.
- Fresh Herbs: Thinly sliced fresh basil adds a bright, aromatic finish. Feel free to use fresh parsley, thyme, oregano, or any combination of your favorite herbs to customize the flavor profile. Fresh herbs truly make a difference in lifting the dish.
- Spices (Salt, Pepper & Italian Seasoning): A light sprinkle of salt and pepper directly inside the hollowed tomatoes is crucial to prevent them from tasting bland, complementing the flavorful stuffing. The Italian seasoning blend (typically including basil, oregano, rosemary, thyme, and marjoram) goes into the filling, infusing it with classic Mediterranean warmth.
- Nutritional Yeast: This is the secret ingredient for that irresistible cheesy flavor in our dairy-free recipe. Just a small amount creates a remarkable umami depth and a cheesy illusion. Beyond flavor, nutritional yeast is a good source of fiber and is often fortified with Vitamin B12, an essential nutrient for vegans.
Choosing the Best Tomatoes for Stuffing
Selecting the right tomatoes is key to the success of this recipe. Larger tomatoes are significantly easier to work with when it comes to coring and filling. Therefore, tiny varieties like grape tomatoes or cherry tomatoes are not suitable for this particular recipe.
The ideal tomatoes for stuffing include:
- Beefsteak Tomatoes: Their large size and firm flesh make them perfect.
- Heirloom Tomatoes: If they are large enough, heirlooms offer a beautiful variety of colors and deep, complex flavors.
- Large Roma Tomatoes (Plum Tomatoes): These are excellent due to their oval shape, firm flesh, and fewer seeds, making them easier to scoop out and hold their shape during baking. San Marzano tomatoes, a type of Roma, are particularly prized for their rich flavor and robust structure.
When shopping, look for tomatoes that are still a bit firm to the touch, have smooth skins free of blemishes, and are relatively uniform in size for even cooking. If your chosen tomatoes have a tendency to wobble, a simple trick is to carefully slice a very thin sliver off the bottom. This creates a flat base, helping them sit securely in your baking dish without tipping over.
As a first choice, always prioritize whatever fresh tomatoes you have growing in your own garden or what’s readily available at your local farmers’ market. These will offer the freshest and most vibrant flavors. “Locally grown” grocery store tomatoes are another excellent option. Remember that prime tomato season generally runs from May through October, so enjoy this recipe when tomatoes are at their peak!
More Healthy Fresh Tomato Recipes
If you find yourself with an abundance of tomatoes (it happens to the best of us!), definitely share your bounty with friends and neighbors. But be sure to save plenty for yourself to try these other delicious vegan tomato recipes:
- Tomato Salad with Balsamic Dressing
- Gluten-Free Tabbouleh
- Summer Pasta Salad
- Fresh Tomato Salsa
- Roasted Tomato Sauce
- Beans and Greens
- Roasted Cherry Tomatoes
- Flatbread with Tomatoes, Pesto and Corn
How to Prepare Baked Stuffed Tomatoes
Quick Tip for Quinoa: If you don’t have pre-cooked quinoa, it’s easy to make! Rinse ½ cup of dry quinoa thoroughly under running water. Transfer it to a small saucepan with 1 ½ cups of boiling water. Reduce the heat to low, maintaining a gentle simmer, and cook for about 15 minutes, or until all the water has been absorbed and the quinoa is fluffy.

The first crucial step is to prepare your tomatoes for baking. Begin by carefully slicing off the top quarter-inch of each tomato. This small incision is all you need to access the interior. For easy and efficient scooping, I highly recommend using a grapefruit spoon or a small paring knife to scoop out the pulp, seeds, and inner membrane, leaving the sturdy outer shell intact.

Decide if you’d like to use the tomato tops for an elegant presentation (to cover the stuffed tomatoes later). If not, dice both the tomato tops and the scooped-out pulp into small pieces and set them aside; they will be incorporated into the flavorful stuffing. Be sure to discard any tough stems and excess seeds. This ensures maximum flavor and minimizes waste.

If your tomatoes aren’t stable enough to sit flat in your baking pan without wobbling, slice a very thin, even piece off the bottom. Be careful not to cut too deeply, which could create a hole that lets the stuffing escape.
Crucially, after scooping, place the hollowed-out tomatoes upside down on a plate. This allows any excess liquid to drain out, preventing your baked stuffed tomatoes from becoming watery and ensuring a perfectly crisp filling.

While your tomatoes are draining, take this opportunity to prep the remaining ingredients. A little “mise en place” (everything in its place) goes a long way here. Once the pan is hot, the filling comes together very quickly, so having all your ingredients chopped, minced, and measured out will make the cooking process smooth and enjoyable. Finely dice your onion and mushrooms, and either mince your garlic or use a microplane for a fine zest.

Heat a heavy skillet (cast iron works wonderfully for even heat) over medium-high heat. Once hot, add a swirl of olive oil. If you prefer an oil-free stuffing, a splash of vegetable broth works perfectly. Sauté the diced onions and mushrooms until they begin to soften and release their moisture, usually about 4-5 minutes.

Next, add the Italian seasoning, the reserved chopped tomato pulp, and the minced garlic to the skillet. Cook for just about 30 seconds, stirring constantly, until the garlic becomes wonderfully fragrant. Be careful not to burn the garlic, as this can impart a bitter taste.

Now, incorporate the cooked quinoa and nutritional yeast into the pan with the sautéed vegetables. Stir everything together thoroughly, allowing the flavors to meld and the quinoa to absorb some of the savory goodness. Continue cooking for a few minutes, stirring frequently, until the mixture is heated through.

Once the filling is heated, turn off the heat. Then, add the chopped greens (like kale) and your fresh herbs (such as basil) to the skillet. The residual heat from the pan will gently wilt the greens, preserving their vibrant color and fresh flavor.

Stir the mixture well until all the ingredients are fully incorporated and the greens have softened beautifully. This incredibly flavorful vegan and gluten-free stuffing is remarkably versatile! Feel free to use any leftover filling to stuff other vegetables like zucchini, bell peppers, mushrooms, or yellow summer squash. Try your best to resist eating too much of this delicious stuffing straight from the pan – it’s truly that good!

Arrange your drained tomatoes, right side up, in a small baking dish. Choose a dish that will hold them snugly, preventing them from tipping over during baking. Lightly sprinkle the inside of each tomato with a pinch of salt and pepper to enhance their natural flavor. Then, use a small spoon to generously fill each tomato cavity with the prepared stuffing. Don’t be shy! If you have any excess filling, tuck it into the crevices between the tomatoes in the baking dish; it will become wonderfully crisp and flavorful as it bakes alongside the tomatoes.

For an extra boost of “cheesy” flavor, sprinkle additional nutritional yeast over the tops of the stuffed tomatoes, if desired. Bake them in a preheated 350°F (175°C) oven for 25-35 minutes. The exact baking time will depend on the size and ripeness of your tomatoes. They are done when the tomatoes are tender but still hold their shape, and the stuffing is piping hot and delightfully crisp on top. Serve immediately and enjoy!
Exciting Stuffed Tomato Variations:
- GREEK STUFFED TOMATOES: To create a Mediterranean-inspired dish, follow the basic recipe. When adding the cooked quinoa, also incorporate one can of cannellini beans (drained and rinsed), ½ cup of chopped Kalamata olives, finely diced bell pepper (any color), and ¼ cup of fresh oregano. This combination adds a burst of tangy, briny, and herbaceous flavors reminiscent of traditional Greek cuisine.
- ITALIAN STUFFED TOMATOES: For an authentic Italian twist, follow the recipe and, when adding the chopped tomatoes to the filling mixture, stir in ¼ cup of toasted pine nuts for a delicate crunch, ¼ cup of dry breadcrumbs (gluten-free if needed) for texture, ¼ cup of dry white wine for depth, and 2 tablespoons of white miso paste. The miso paste adds an incredible depth of umami, enhancing the savory Italian flavors without being overtly “miso-like.”
- MAIN COURSE STUFFED TOMATOES: To transform this side dish into a complete and hearty main course, simply follow the existing directions but include an additional 1 cup of cooked lentils or beans (such as chickpeas or black beans) into the stuffing recipe. Use super-large tomatoes to accommodate the extra filling and increase the baking time by approximately 10 minutes to ensure everything is thoroughly cooked and tender. This makes for a robust and satisfying meal on its own.
- SPICY STUFFED TOMATOES: If you love a kick of heat, chop some jalapeños or serrano peppers (removing the seeds for less heat, or leaving some in for more) and add them to the pan with the onions and mushrooms during the sautéing process. For an even spicier rendition, you can also mix in ½ teaspoon of red pepper flakes or ¼ teaspoon of cayenne pepper along with the Italian spices. Adjust the quantity to your preferred spice level.
Meal Prep and Storage Tips
- SERVE: These versatile vegan stuffed tomatoes can be enjoyed in many ways. They make a fantastic light lunch, a flavorful and healthy side dish to accompany your favorite plant-based proteins, or a satisfying vegan main course on their own. They’re also excellent served at room temperature, making them ideal for potlucks and picnics.
- PREP AHEAD: To save time, you can prepare the stuffing mixture in advance and store it in an airtight container in the refrigerator for up to 3 days. Similarly, hollow out the tomatoes and store them separately in the fridge. When you’re ready to bake, simply stuff the tomatoes and follow the baking instructions. Alternatively, you can fully prepare and bake the recipe, then store the cooked stuffed tomatoes, tightly covered, in the fridge for up to 3 days, reheating as directed.
- STORE: Leftover baked stuffed tomatoes should be stored in an airtight container in the refrigerator. They will remain fresh and delicious for up to 5 days. When reheating, place them in a preheated 350°F (175°C) oven for approximately 20 minutes, or until they are heated through and the filling is warm.
- FREEZE: The stuffing itself freezes very well. You can make a larger batch of the quinoa and mushroom filling and freeze it in an airtight container for future use. However, I generally do not recommend freezing the *stuffed tomatoes* themselves. Fresh tomatoes tend to become very watery and lose their firm texture when defrosted, making the final dish less appealing. For the best texture and flavor, it’s best to stuff and bake the tomatoes fresh.
Debra’s Pro Tips for Perfect Stuffed Tomatoes

- Don’t Skip the Draining Step: After scooping out the tomato pulp, remember to turn the hollowed-out tomatoes upside down on a plate. This seemingly small step is crucial! It allows any excess liquid to drain out, preventing your tomatoes from becoming watery during baking. If you realize you forgot this step after making the stuffing, use a paper towel to carefully blot and sop up any remaining liquid from the tomato cavities before filling them. This ensures a firmer tomato and a crispier, more flavorful stuffing.
- Mindful Trimming for Stability: When trimming a thin slice off the bottom of your tomatoes to help them sit flat in the baking dish, be very careful not to cut all the way through the tomato. A hole at the bottom will cause your delicious stuffing to leak out during baking, leading to a messy dish and lost flavor. Aim for just a thin, even slice to create a stable base.
- Stuff Generously for Maximum Flavor: Don’t be shy when filling your tomatoes! Pack them as full as you possibly can. The generous amount of stuffing is truly the best part of this dish, offering a satisfying texture and bursting with all the incredible flavors. The more stuffing, the more enjoyable each bite will be!
More Healthy Stuffed Vegetable Recipes You’ll Love
- Meaty Vegan Stuffed Zucchini Boats
- Vegan Stuffed Peppers with Lentils
- Gluten-Free Stuffed Mushrooms
- Stuffed Butternut Squash Recipe
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📖 Recipe

Vegan Stuffed Tomatoes
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Ingredients
- 2 lbs tomatoes
- ¼ teaspoon coarse sea salt
- ¼ tsp black pepper
- ½ cup yellow onion finely diced
- ½ cup shitake mushrooms finely diced
- ½ teaspoon coarse sea salt
- 1 tsp dried Italian seasoning
- 6 cloves garlic minced
- ¼ cup nutritional yeast
- 1 ½ cups cooked quinoa
- ½ cup kale roughly chopped
- ¼ cup fresh basil finely chopped
Instructions
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Preheat oven to 375°F (190°C).
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Carefully cut off the top ¼ inch of each tomato. Using a grapefruit spoon or small paring knife, gently scoop out the insides of the tomatoes, ensuring the outer shell remains intact. Sprinkle the inside of each hollowed tomato with salt and pepper. Place the tomatoes upside down on a plate to drain excess liquid while you prepare the filling. Roughly chop the scooped-out tomato pulp and the tomato tops, setting them aside to use in the stuffing.
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Heat a large skillet over medium-high heat. Add a swirl of olive oil (or vegetable broth for an oil-free option). Sauté the diced onions and mushrooms for about 4 minutes until they begin to soften. Sprinkle in the ½ teaspoon coarse sea salt and Italian seasoning, then stir well. Add the chopped tomato pulp and minced garlic. Cook for an additional 30 seconds, stirring constantly, until the garlic is fragrant.
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Turn off the heat. Stir in the nutritional yeast, cooked quinoa, chopped kale, and fresh basil. Continue to mix thoroughly until the greens are fully incorporated and have wilted from the residual heat.
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Taste the quinoa mixture and adjust seasoning as needed, adding more salt and pepper to your preference.
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Place the drained tomatoes right side up in a baking dish that will hold them snugly. Using a small spoon, generously fill the inside of each tomato with the prepared stuffing mixture. If you have any extra filling, spoon it into the spaces between the tomatoes in the baking dish.
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Bake for 25-35 minutes in the preheated oven. The tomatoes are done when their skins begin to soften and crack slightly, and the filling is heated through and crisp on top. Larger tomatoes may require a few extra minutes of baking time.
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Serve warm immediately, or enjoy at room temperature.
Notes
Reheat: To reheat, place them in a preheated 325°F (160°C) oven for about 15 minutes, or until thoroughly heated through.
Nutrition
Note
The nutrition calculations were done using online tools. To obtain the most accurate representation of the nutritional information in any given recipe, you should calculate the nutritional information with the actual ingredients you used. You are ultimately responsible for ensuring that any nutritional information is accurate, complete and useful.