Mac and Cheese Muffins – Two Ways
(Gluten-Free & Vegan OR Classic Comfort)
There’s something so fun about taking a nostalgic favorite and giving it a fresh twist. Mac and cheese will forever be the comfort food of all comfort foods—but in muffin form? Even better. These little cups are portion-controlled, golden on top, and packed with cheesy goodness.
And because I couldn’t decide which version I loved more, I made two: a lighter Vegan & Gluten-Free version for when you want to keep things plant-based, and a Classic Whole Wheat version for when you’re craving the real-deal cheesy indulgence.
Whether you’re serving these as appetizers, a side dish, a light main dish, or a cozy snack, they’re guaranteed to disappear fast.
Mac n' Cheese Muffins
Rate This Recipe:
Equipment
- 2 large pots
- 1 medium saucepan
- 1 Small Skillet
- Whisk
- Mixing spoons/spatula
- Muffin tins
- Small Bowl
- box grater
Ingredients
Option 1: Vegan & Gluten-Free Mac and Cheese Muffins
- 1 lb gluten-free elbow macaroni
- 4 tsp olive oil
- 1 shallot finely diced
- 2 cloves garlic minced
- 1½ cups unsweetened plant-based half-and-half (such as Ripple, Nut Pods, or Silk)
- 1½ cups unsweetened almond milk
- 1 tbsp white vinegar
- 3 tbsp vegan butter (preferably organic)
- 5 tbsp gluten-free all-purpose flour (such as Bob's Red Mill 1:1)
- 1 lb vegan sharp cheddar cheese grated (such as Violife or Daiya)
- ½ lb vegan Gruyère grated (optional, or use more Cheddar)
- 1 tbsp coarse sea salt
- ½ tsp black pepper
- 3 large heirloom tomatoes diced
- ¼ cup gluten-free seasoned breadcrumbs
- 3 tsp fresh thyme leaves minced
Option 2: Classic Whole Wheat Mac and Cheese Muffins
- 1 lb whole wheat elbow macaroni
- 4 tsp olive oil
- 1 shallot finely diced
- 2 cloves garlic minced
- 1½ cups half-and-half
- 1½ cups 1% milk
- 3 tbsp unsalted butter (preferably organic)
- 5 tbsp whole wheat flour
- 1 lb reduced-fat sharp Cheddar cheese grated
- ½ lb Gruyère cheese grated
- 1 tbsp coarse sea salt
- ½ tsp black pepper
- 3 large heirloom tomatoes diced
- ¼ cup seasoned dried breadcrumbs
- 3 tsp fresh thyme leaves minced
Instructions
Directions are the same for both versions
- Preheat oven to 375°F. Coat muffin tins with cooking spray.
- Cook pasta until just al dente. Drain and set aside.
- Sauté aromatics: In a small skillet, heat 1 tsp olive oil and cook shallot + garlic until translucent.
- Warm milk mixture: Combine half-and-half + milk (or plant-based versions) and vinegar if vegan. Warm gently (don’t boil).
- Make roux: In a large pot, melt butter (or vegan butter) with olive oil. Whisk in flour until lightly golden.
- Build sauce: Add shallot mixture + warmed milk to roux. Whisk until creamy.
- Add cheese: Stir in cheeses until melted. Season with salt + pepper.
- Combine: Stir pasta + diced tomatoes into the sauce.
- Fill muffin tins: About ¾ full. Top with breadcrumb mixture (breadcrumbs + olive oil).
- Bake: 30–35 minutes, until bubbly and golden. Cool 5 minutes before serving. Garnish with fresh thyme.
More About This Recipe
Kitchen Tips
- Don’t skip the cooling time—5 minutes helps them hold their muffin shape.
- Grating cheese fresh (vegan or dairy) always melts better than pre-shredded.
- These freeze beautifully! Just wrap tightly and reheat in the oven at 350°F for 10 minutes.
Kitchen Tools You’ll Need
- Large pot – to cook the pasta.
- Small skillet – for sautéing the shallot and garlic.
- Medium saucepan – to warm the milk mixture.
- Large pot or Dutch oven – for making the roux and combining everything into the cheese sauce.
- Whisk – essential for a smooth, creamy sauce.
- Mixing spoons/spatula – to fold in pasta and tomatoes.
- Muffin tins – disposable aluminum pans or standard tins, 12-cup each.
- Small bowl – for mixing the breadcrumb topping.
- Box grater – to shred cheese (dairy or vegan) for best melting.
Nutrition
Why You’ll Love These Mac n’ Cheese Muffins
- Plant-based or classic—you choose! The vegan/gluten-free version is easier on digestion and lighter in saturated fat, while the whole wheat version brings more fiber and that traditional cheesy richness.
- Tomatoes bring the glow. Rich in vitamin C and lycopene, great for skin health and immunity.
Final Thoughts
Whether you go for the lighter vegan & gluten-free version or the classic cheesy whole wheat, these Mac and Cheese Muffins are such a fun way to enjoy comfort food in perfectly portioned bites. They’re cozy, versatile, and guaranteed to bring smiles around the table.
I’d love to know — which version would you make first? Or do you think you’ll try both? Share your thoughts in the comments, and if you bake these, don’t forget to tag me so I can see your delicious creations!