Even though all eating options are often compared, in the case of these flours, it is important for you to assess what your priorities are. People who wish to lose weight ardently and wish to shed immense amounts of weight should opt for bajra flour because of its relatively lower calorie content even though both are gluten free options. However, if consumed too often, it can lead to the development of kidney stones in people who have tendencies to develop them. Phytic acid present in bajra can also lead to problems in absorption of food in the gut.
In case of maize, people who have a tendency for developing blood clots and thrombosis should refrain from consuming too much of it. Since it is difficult to digest it can also cause digestive problems like bloating, gas and diarrhea. After carefully considering these adverse effects and weighing out the advantages of the two flours, you should decide on the more suitable option for you.