For croutons: Place all ingredients into a bowl and toss together until evenly coated. Pour croutons into a large skillet and place over medium heat. Toast croutons for 5 to 7 minutes, stirring frequently. Remove from heat and allow to cool and crisp. Set aside until ready to use.
For soup: Pour oil into a medium pot and place over medium-high heat. Add onion and leek and sauté for 3 to 4 minutes or until onions and leeks become translucent. Add garlic, carrots and celery and season with salt and pepper.
Sauté for 4 to 5 minutes and stir in 2 tablespoons thyme. Add beer and broth and simmer for 8 to 10 minutes or until vegetable mixture is fork tender. Remove from heat and set aside.
In another medium pot melt butter. Whisk in flour to create a roux and continue to whisk for 2 to 3 minutes. Whisk in milk until no lumps remaining and mixture thickens. Stir in pumpkin puree until smooth. Toss cheese together with lemon juice before stirring into the milk mixture. Stir until cheese sauce is smooth. Stir in remaining spices.
Pour cheese mixture and broth mixture into a blender and blend until smooth. Pour mixture back into a pot and simmer for 3 to 4 minutes or until soup thickens slightly. Stir in remaining thyme and adjust seasonings.
Ladle soup into bowls and top with buttered croutons. Serve.