The awards, sponsored by Britvic Soft Drinks in association with the UK's Periodical Publishers Association, reward excellence in journalism in the food and drink sector.
At a ceremony at London venue Titanic on Friday, Martin Paterson, former deputy general of the Food and Drink Federation, said: "NutraIngredients.com has a fantastic eye-catching homepage with outstanding interactivity throughout. Its excellent news and analysis pages contained links to important information and other websites."
The judging panel, drawn from the media and the food and drink industry, looked for innovation, use of technology, demonstration of commitment, news research and insight. Interactivity, ease of use and breadth of audience were also essential.
The award was presented to editor Jess Halliday by member of parliament Charles Kennedy, the former leader of the UK's Liberal Democrat party.
Decision News Media journalist Chris Mercer was also honored as a finalist in the Newcomer of the Year category.
Paterson said Mercer is "obviously a journalist who has a knack of finding a scoop, an excellent array of contacts and is able to deliver copy in a clear and concise style".
This is the second year in a row that a website published by Decision News Media (formerly Novis Group) has received the Website of the Year award. Last year it went to sister site FoodNavigator.com.