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Step 1
Mince 2 garlic cloves and finely chop 1/2 medium yellow onion.
Step 2
Heat 1/4 cup extra-virgin olive oil in a 12-inch skillet over medium heat until shimmering. Add the onion and garlic and cook, stirring occasionally, until softened but not browned, 3 to 4 minutes.
Step 3
Add 1 teaspoon red pepper flakes, 1/2 teaspoon kosher salt, and 1/4 teaspoon black pepper and continue cooking until the onion mixture turns golden-brown, about 1 minute more.
Step 4
Add 1 (28-ounce) can crushed tomatoes and stir to combine. When the mixture begins to bubble and splatter, lower the heat as needed to maintain a simmer and continue cooking until the sauce is flavorful and no longer raw tasting, about 20 minutes. Meanwhile, finely grate 1/2 ounce Pecorino Romano or Parmesan cheese (about 2 tablespoons). Cut 1/4 cup loosely packed fresh basil leaves into strips as thin as possible.
Step 5
Using a spoon, create a depression to the best of your ability in the tomato sauce. Crack 1 large egg into the depression, then spoon some of the tomato sauce over the egg to cover. Repeat with the remaining 5 eggs, spacing them evenly apart in the pan.
Step 6
Cover and cook on medium heat until the whites are just set, 6 to 8 minutes for runny yolks (cook longer for set yolks). Uncover and sprinkle with the cheese and basil. Divide between 3 to 4 bowls and serve with crusty bread.