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mac and cheese in muffin cups set on a wood board

Healthy Spinach Artichoke Mac ‘n Cheese Cups

  • Author: Lauren Grant
  • Prep Time: 10 minutes
  • Cook Time: 35 minutes
  • Total Time: 45 minutes
  • Yield: 12 cups 1x
  • Category: Main dish
  • Method: Baking
  • Cuisine: American
  • Diet: Vegetarian


Healthy macaroni and cheese gets made over into individual cups. Packed with the flavors of spinach and artichoke dip, these mac and cheese cups are perfect for meal prep, served as an app, or a fun weeknight dinner.


  • 8 ounces bean-based elbow or shell pasta, such as Banza
  • 2 tablespoons unsalted butter, divided
  • 2 tablespoons olive oil
  • 1 (14-ounce) can artichoke hearts, drained and roughly chopped
  • ½ cup diced yellow onion
  • 2 tablespoons whole-wheat flour
  • 1 teaspoon minced fresh garlic 
  • 1 ½ cups milk, warmed
  • Cracked pepper and kosher salt
  • ¼ cup whole-milk Greek yogurt  
  • 2 teaspoons Dijon mustard 
  • 1 cup grated Gouda cheese 
  • ½ cup grated fontina cheese
  • 1 (6 ounce) bag fresh spinach, chopped 
  • ¼ cup Panko bread crumbs  


Preheat oven to 425ºF. Line a 12-cup standard muffin tin with paper liners or coat with nonstick spray; set aside.

Cook pasta in a large saucepan or pot of boiling salted water for 2 minutes less than package directions, drain and toss with a splash of olive oil to avoid sticking. 

In a large pot or Dutch oven, heat 1 tablespoon butter over medium high. Add artichokes and sauté until lightly browned, 4–5 minutes. Transfer browned artichokes to a small bowl; set aside.

Add 2 tablespoons olive oil to now-empty pot over medium heat, add onion and cook until softened, about 4 minutes. Sprinkle in flour, garlic, ½ teaspoon pepper and ¼ teaspoon salt; cook, whisking constantly, until flour turns golden brown, 1 minute. 

Gradually pour in milk, whisking constantly, until no lumps of flour remain. Bring sauce to a simmer and cook until thickened, about 5 minutes.

Whisk in yogurt and Dijon. Add Gouda and Fontina by small handful, whisking to incorporate after each addition. Remove pot from heat and stir in cooked pasta, cooked artichokes and spinach. Season with salt and pepper to taste.

Microwave remaining tablespoon butter in a small bowl microwave-safe bowl until melted. Add Panko and stir to combine; season with salt and pepper to taste.

Divide mac and cheese between prepared muffin wells and sprinkle each with breadcrumbs. Bake mac and cheese cups until topping is deep golden brown, 10–12 minutes. Let rest in pan 5 minutes before serving.


Milk: I recommend whole milk or 2% milk. Skim milk will work but the mac and cheese won’t be as creamy. Nut milk will also work, I recommend unsweetened and unflavored soy, almond or macadamia nut milk. 

Gouda: Aged Gouda is one of my favorites here, but smoked is also great. And if Gouda isn't your thing, you can use a sharp Cheddar cheese instead.

Pasta: Don't like bean pasta or can't find it? Use regular or whole-wheat elbow macaroni or shell pasta.

Leftovers: store leftover mac and cheese cups in an airtight container in the refrigerator for up to 4 days. Reheat in the microwave for 30–60 seconds or in a 300-degree oven until warmed through.

Keywords: mac and cheese cups, mac and cheese muffins

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