The "no artificial colours" message will be featured on Smarties packs, special display materials and a television ad campaign trumpeting the move, created by JWT, will be unveiled this summer.
The move follows claims by health campaigners that artificial colours and flavourings in sweets make children hyperactive and fuel temper tantrums.
As a result of the change, blue Smarties are being dropped from next month because Nestle can not find a way to make the chocolates turn this colour without using artificial colouring. They will be replaced with a white Smartie.
Birte Leiner, Nestle Rowntree's senior brand manager, said: "Removing artificial colours is a significant move, which will provide parents with even greater assurance in choosing the Smarties brand."
Smarties is the second Nestle brand to become free from artificial colours, after the entire Rowntree range made the move in summer 2005.
Nestle dropped the round Smarties tube in favour of hexagonal tube last summer.
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