The scheme is being trialled at four stores with the aim to roll it out at a national level across the 121 stores. The pots will be re-used where possible or shredded into base material and used to make new products.
The company has also launched Plan Apple, an action programme aimed at "addressing sustainable development challenges" facing the gardening industry.
Wyevale sustainability director Dr Alan Knight has identified 10 areas where environmental and social trends overlap with garden centre concerns.
Wyevale's "10 Commitments" are areas where the company plans to focus its environmental and sustainability efforts.
They include working with nature and connecting with food sources, reducing waste and unnecessary packaging, using less water, protecting endangered forests and peat bogs, ensuring that suppliers benefit properly wherever products are sourced, inspiring sustainable lifestyles and the encouragement of carbon-positive gardening.
Each commitment is backed by action programmes, which will be gradually implemented over the next two years.
Knight said: "Wyevale's central aim is to make it easier for our customers to live more sustainably through their lifestyles and the way they use their gardens."
The commitments outlined what has to be done to deliver that aim, he added.
"We need everyone to work with us on this if we are to succeed - and that is our challenge to the industry. "
Wyevale chairman Jim Hodkinson said: "Plan Apple will demonstrate that we are serious about adhering to a meaningful green agenda to guide our future development."