In a large pot, bring water to a boil and cook the green beans for about 5 minutes, until tender but still crisp. Drain and set aside.
In a large skillet, heat the olive oil over medium heat. Add the onions and cook until translucent, about 5 minutes. Add the mushrooms and garlic, and cook for another 5 minutes.
Sprinkle the flour over the vegetables and stir well to combine. Slowly add the vegetable broth and almond milk, stirring constantly until the mixture thickens, about 5 minutes. Season with salt and pepper to taste.
Combine the green beans with the mushroom sauce and mix well. Transfer the mixture to a baking dish and top with fried onions.
Bake in the preheated oven for 20-25 minutes, until the top is golden brown and bubbly. Serve hot.