Cook pasta in salted water according to package directions.
In a medium pot, melt butter over medium heat. Once completely melted, whisk in flour until it forms a smooth paste.
Slowly stream in milk, whisking well, until completely incorporated. Let simmer for a few minutes until it starts to thicken, stirring occasionally to prevent burning.
Add in salt, pepper and vegan cheese and stir well. Vegan cheese takes a bit longer to melt, so keep stirring over medium heat until fully incorporated into a cheesy sauce.