This follows a six-month review of Nestle's £60 million UK media planning and buying arrangements between its two incumbent agencies.
With the coffee business added to its £25 million confectionery assignment, MindShare now handles the bulk of Nestle's account.
Universal has retained the company's chilled dairy range with brands including Munch Bunch yogurts, the Herta meats range of products and the Nesquik accounts.
Nestle's cereal business, which produces brands including Cheerios and Golden Nuggets, was not included in the review as it is part of a joint venture with Cereal Partners.
Although Universal has retained some of the account, the loss of the coffee business will come as a major blow. Universal was responsible for establishing the recent long-term sponsorship deal between Nescafe Channel 4's flagship youth soap opera, Hollyoaks.
"This is a huge win for MindShare. There is nothing more rewarding than winning new business from an existing client," Kelly Clark, the chief executive of MindShare, said.
The review was overseen by Stuart Cox, the Nestle media manager, along with the communications and corporate affairs director, David Hudson, and the media consultant, Philip Buckman.
Hudson said: "The review has given us the opportunity to encourage creative media thinking by both agencies, and has resulted in Nestle having a strong vision for the future of our media planning and buying in the UK."