Cheese sauce almost always turns grainy because of excessive heat. At high temperatures, the cheese’s protein network contracts instead of loosening; it clumps into small curds and releases the fat it was holding. The sauce looks both grainy and greasy. To prevent this, add the cheese gradually to a warm base removed from the heat, rather than to a boiling mixture, and use a starch-thickened base.
When cheese warms, its fat melts first, then its protein network loosens and the cheese flows. But once the temperature passes a certain point, the network stops loosening and contracts instead; protein molecules bind tightly to one another and form small clumps. The same contraction also pushes out the fat held in the network. The result is a sauce that is both grainy and topped with pools of oil. That is why graininess is related to heat control rather than the quality of the cheese. Even a sauce made with expensive cheese can easily be ruined by the same mistake.
The most common mistake when making cheese sauce is adding the cheese to a boiling mixture. Shredded cheese added while the pot is bubbling will clump before it even sinks to the bottom. The right method is to prepare the base, take the pot off the heat, then add the cheese a handful at a time, stirring each addition until it melts. If needed, warm the mixture over very low heat, but do not let it boil. The same rule applies to fondue and cheese soup: add the cheese last. For the same reason, do not return the pot to the heat after adding the cheese.
The second precaution is the base. Adding the cheese to a base lightly thickened with starch or flour produces a much more stable sauce than adding it directly to milk or cream. Starch gets between protein molecules and makes it harder for them to bind tightly to one another. This is why cheese sauces made with a béchamel base are less likely to become grainy; the flour does more than thicken the sauce—it also helps protect it. If a recipe calls for starch or flour, do not skip that step.
The third precaution is choosing the cheese. Use a good, medium-aged cheese; very aged, dry cheeses are already prone to separating when heated. Finely shred the cheese, because larger pieces contract on the outside before they melt. Shred block cheese fresh; the starch in pre-shredded cheese can actually help in this recipe. Do not let the cheese sit after shredding; an exposed pile dries out and clumps. Choose a grater with large holes so the cheese melts more slowly and you have time to stir.
A grainy sauce can often be saved. Take the pot off the heat, add a few spoonfuls of hot milk or cream, and whisk vigorously. If that is not enough, blend the sauce with an immersion blender; the clumps will break up and the mixture will become smooth again. Starch dissolved in 1 spoonful of cold milk can also be added as a binder; if you do, heat the mixture briefly. Do not boil a rescued sauce again; serve it right away. If it needs to wait until serving, keep it warm over a bowl of hot water and do not return it to the stove.