Nutritional yeast is best consumed in small amounts daily.
Nutritional yeast is a very high source of niacin (Vitamin B3). The tolerable upper limit (TUL) for niacin is set at 30 mg per day because some people experience uncomfortable facial flushing after consuming anywhere from 30-1000 mg of niacin per day. One tablespoon of nutritional yeast provides 28 mg niacin which puts it very close to the tolerable upper limit. Flushing is a transient symptom that goes away when excess niacin is removed from the diet. If you do not experience flushing as an unwanted side effect, you can go beyond this limit. In one case somebody experienced significant flushing after eating 15 tsp of nutritional yeast (140 mg niacin).
Liver toxicity has been observed when consuming 3,000 mg niacin (Vitamin B3) per day. In order to receive this amount of niacin, one would need to consume 100 tbsp (850 grams) of nutritional yeast per day, which is unlikely.
Another reason to consider limiting nutritional yeast intake is purines. Japan recommends limiting daily purine intake to 400 mg to prevent gout. The same study measured purine content in brewer's yeast product (not nutritional yeast) and found it to have 1200 mg/100 g. If nutritional yeast has the same profile as beer yeast product, then the recommended daily amount would be 30 g, or about 4 tbsp.