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Step 1
Fill a large pot with water and bring to a boil. Add a small handful of salt and the shells and stir. Bring the water back up to a boil and cook shells for 7 to 9 minutes or until al dente (soft with a slight bite), stirring occasionally. Strain shells and set aside until ready to use.
Step 2
Place a 10 inch skillet over medium heat and melt butter. Sprinkle flour into skillet and stir until well combined and the raw flour taste disappears, 2 to 3 minutes.
Step 3
Stir in milk and continue to stir until no lumps remain. Lower heat to medium-low and allow mixture to thicken, enough to coat the back of a wooden spoon. Stir in mustard until well combined. Season with salt and pepper.
Step 4
Remove pot from heat and begin stirring cheeses into the skillet, a little at a time (waiting for cheese to fully melt before adding more) and continue to stir together until all the cheese has been added and mixture is thick and smooth.
Step 5
Fold in the cooked and cooled shells until just combined and adjust seasonings as needed.
Step 6
Heat broiler to high.
Step 7
In a small bowl toss together crushed crackers butter and thyme until well combined. Top the mac and cheese filled skillet with the buttered cracker mix and place under the broiler for 1 to 2 minutes or until the shells slightly caramelize and the cheese sauce becomes hot and bubbly. (you can also transfer the mixture into individually-sized buttered skillets and top with the cracker mixture before placing under the broiler).
Step 8
Allow the mac and cheese to sit and cool for 5 to 7 minutes before serving.