Meanwhile, heat the olive oil in a large skillet over medium heat.
Add the onion and cook for 3 minutes, until softened.
Stir in the garlic and cook for 30 seconds.
Add the almond milk, chipotle peppers, Dijon mustard, and smoked paprika.
Simmer for 2 minutes.
Reduce the heat to low and stir in the cheddar, mozzarella, and Greek yogurt until smooth.
If needed, add a splash of the reserved pasta water to loosen the sauce.