The Department of Health and Mental Hygiene said the voluntary change could also help fight the city's biggest killer, heart disease.
To comply, chefs would have to dump many margarines and frying oils, and possibly reworking long-held recipes for baked goods.
CBS News Correspondent Elizabeth Kaledin reports that some New York restaurants, like the Comfort Diner, have already made the switch to soybean oil. It's more expensive, but owner Ira Freehoff says it's worth it.
"About ten years from now, your heart would be able to tell the difference," Freehoff told Kaledin.
The New York State Restaurant Association supports the effort, Executive Vice President E. Charles Hunt said in a health department release Wednesday.
The fats, found in partially hydrogenated vegetable oils, raise diners' chance of developing heart disease in much the same way that saturated meat and dairy fats do, raising overall and bad cholesterol while lowering good cholesterol, American Heart Association President Robert Eckel said in the release.
The Food and Drug Administration has already targeted trans fats. Nationwide, all foods containing the chemically modified oils must be labeled beginning next January.
Some workers and diners were skeptical of the city plan.
"Labeling is as far as you want to go. You don't want to be telling people what to eat," Brooklyn waitress Karen Quam told The New York Times.
The city's request came two years after it outlawed smoking in bars, restaurants and offices, citing concerns about the ill effects of secondhand smoke.