A method of making a processed cheese with improved firmness comprises mixing a protein cross-linking enzyme and optionally first other ingredients with a cheese material having a pH of less than 5.6, a moisture content of less than 60% and preferably containing one or more coagulating agents, to form a mixture; providing temperature and pH conditions and allowing time for the enzyme to react with protein in the mixture to cross link at least a portion of the protein; and combining one or more emulsifying agents and optionally second other ingredients with the mixture and heating the combination to thereby produce processed cheese from the combined cheese material contain cross-linked proteins, emulsifying agents and optional first and second other ingredients.