We have only made the muffins with regular all purpose flour and gluten-free measure-for-measure flour. Whole wheat flour is great in terms of protein content but it can make baked goods denser and require more moisture to be added. This batter is a thicker batter to start with so we don't recommend swapping the full flour amount for whole wheat. The rule of thumb about swapping whole wheat flour into a recipe is that you can use up to half the flour (in this case half is 1 1/4 cups) as whole wheat and the other half all purpose flour without adjusting other ingredients.