Two sources said the rollout would occur once locations deplete the supply of liquid margarine.
McDonald's did not respond to CNBC's requests for comment.
Read MoreMcDonald's quietly changes its Quarter Pounder size
One sign at a Manhattan location says, "We're proud to cook breakfast items on the grill with real butter and we toast our English Muffins, biscuits and bagels with real butter too."
The signs are meant to both highlight the "real dairy" addition and warn those who are not able to eat items made with milk products.
The move is just the latest in a series by the fast food giant aimed at tweaking the way it makes its food as it continues trying to turn around its struggling U.S. business. As part of the overhaul, McDonald's has said it would toast its buns longer, change how it sears and grills its beef, and increase the Quarter Pounder patty size.