The eco-friendly bottles are made of polylactic acid - an annually renewable source from corn - in a carbon neutral process, where no greenhouse gases are produced. They compost completely in 40 days.
Initially, the new bottles will contain the brand's yoghurt, vanilla bean & honey thickie from September, but they will be rolled out to the rest of the range later in the year.
The new packaging follows the arrival of similar bottles in Waitrose from water brand Belu, which donates its net profits to Third World charities.
Innocent's move is part of a drive to reduce the environmental impact of the 500,000 tonnes of plastic bottles buried in the UK each year. Co-founder Richard Reed said he hoped it would encourage other manufacturers to look at the impact of their packaging.