Add bacon to a medium skillet over medium heat. Cook, stirring occasionally, until bacon is crisp, about 8-10 minutes. Transfer with a slotted spoon to a paper towel-lined plate. Use accumulated bacon fat from the skillet to grease a standard 12-cup muffin tin.
In a large bowl, whisk to combine eggs, milk, and coconut flour. Season with salt and pepper. Add spinach and bacon and stir to combine. Divide among muffin tins and top with ricotta and pesto.
Transfer to oven and bake until just cooked through, about 14-16 minutes. Serve warm or at room temperature.