Cover the dough with aluminium foil or a clean cling film before storing it in a container and refrigerating it. Cover the dough completely so there are no air bubbles left.
Store your dough in a zip lock bag or an air-tight container as well before placing it in the fridge, it prevents spoiling.
Too much water while kneading the dough can make it spoil faster. Make sure you add water in small quantities and balance the consistency by adding dry flour.
Covering the dough with a layer of oil or ghee before refrigeration can keep it off from spoiling. The greasy layer may prevent blackening and drying of the atta.