The 56-year-old took home £1.4million for 2015, up from £991,000 a year earlier at the company, which makes Cathedral City cheese.
Allen, who lives in a five-bedroom house in Surrey worth £1.2million, earned a salary of £523,000 and received £120,000 in pension contributions.
His benefits, which include a car allowance, life insurance, and private healthcare, amounted to £32,000.
It comes after Dairy Crest saw profits fall from £54.2million to £22.1million.