In a large bowl with a wooden spoon or in a stand mixer fitted with the dough hook, combine the flour, yeast and salt. Add the water and beer. Mix until the dough forms a soft ball. On a lightly floured work surface or in the stand mixer, knead the dough for 5 minutes or until smooth.
Form the dough into a ball and place in a clean, lightly oiled bowl, turning to coat with the oil. Cover with a damp cloth and let rise in a warm, humid spot for 2 hours or until doubled in volume.
Meanwhile, in a large skillet over medium-low heat, soften the onions in the oil until translucent. Set aside in a bowl.
Place a pizza stone or inverted baking sheet on the middle rack of the oven. Preheat the oven to 500°F (260°C).
Divide the dough into 2 equal parts. On a lightly floured work surface, roll out one piece of dough to form a 15 x 10-inch (38 x 25 cm) oval. Place on a sheet of parchment paper. Repeat with the second piece of dough. Cover with an inverted baking sheet or plastic wrap and let rest for 15 minutes.
Spread the crème fraîche over the dough. Generously season with pepper. Top with the onions, bacon and cheese.
Place 1 flammekueche at a time (with the parchment paper) on the pizza stone. Cook for 8 to 10 minutes or until the dough is cooked and golden and the toppings are beginning to caramelize.
Recipes with the "Healthy Pick" stamp have been evaluated by a registered dietitian member of the Ordre professionnel des diététistes du Québec.