The sector's most prestigious awards, sponsored by Britvic Soft Drinks in association with the UK's Periodical Publishers Association, reward excellence in journalism, focusing particularly on clarity, balance and fairness, content, originality and evidence of research.
In naming FoodNavigator.com as the winner of the website of the year awards, the judges said it was "a great site".
"It is easy to manoeuvre with plenty of interactive technology and does not rely on a magazine for stories", they said.
Announcing the awards in London on Friday, Lizzie Kershaw, executive group publishing director of the Good Housekeeping and Country Living Group, said in choosing the website of the year, the judges had additionally looked for commitment and insight to research and news; interactivity and breadth of audience; and innovation and use of technology.
The award was presented to FoodNavigator.com editor, Lindsey Partos, by Piers Morgan, former editor of The Daily Mirror.
The judges also Highly Commended website finalist irn-talkingshop.co.uk, as "an easy to follow site, packed with plenty of relevant day-to-day information", and named just-drinks.com as the third finalist for the award.
Novis journalist, Dominique Patton, the editor of NutraIngredients.com, was additionally named as a finalist in the awards - short-listed alongside journalists from The Grocer, The Publican, The Morning Advertiser Scotland and Off-Licence News - as news reporter of the year.
Looking for "evidence of knowledge, tenacity and research; genuine exclusives; and a consistent demonstration of commitment to news generation", the panel said Dominique was "an industrious journalist, grafting effectively in a specialised market, unearthing very specific data."
This year also brought a strong endorsement for Independent Retail News, which won awards both as the publication of the year, and for editor of the year.
The 12-member judging panel, drawn from the media and the food and drink industry, included the chairman of the UK's Periodical Publishers Association, the deputy director-general of the Food and Drink Federation and six senior media editors, including the associate editor of BBC Good Food.