The appointments are likely to signal a less traditional approach to marketing for the high-street retailer, which is modernising its business in the face of competition from supermarkets.
Although Boots The Chemist's sales were up by 3.6% in the six months to September 30, the company has struggled for some time and a new management team has been installed to focus on customers.
The agencies will start on April 1, with the first work breaking in the spring. Mother was awarded the business following a final pitch against incumbent J Walter Thompson, after Publicis and Abbott Mead Vickers BBDO were eliminated from the shortlist last week. Naked and MediaCom take on the media job from MindShare, handling media planning and buying respectively.
Naked will also work with Mother on developing strategic thinking.
Mother pitched with a team of agencies that included DM firm Craik Jones Watson Mitchell Voelkel, Mother-owned branding consultancy Saturday, digital agency Poke, PR agency Cake and marketing agency Circus. A Boots spokesman said that it had not been decided whether these agencies would be awarded any work.
The appointments follow a three-month process which took a dramatic turn when chief executive Richard Baker axed marketing director Ann Francke from her role mid-pitch.
Boots chief commercial officer David Kneale is now responsible for marketing.
He said: "It was a tough decision. We have had a great relationship with JWT and MindShare over the years."