Heat oil in a large pot over medium heat. Cook garlic and leek until soft and translucent, about 4 minutes. Add apple, celery, and ginger, and cook for 3 minutes. Add sweet potatoes and stock, and simmer until sweet potatoes are tender, about 15 minutes. Add chipotle chile.
Working in batches, transfer mixture to a blender, and puree until smooth, transferring soup to a large bowl as you work. (For safety, remove cap from hole in lid, and cover with a dish towel to prevent spattering.) Season with salt and pepper. Sprinkle with pepitas before serving.