Gove replaces former Defra Secretary Andrea Leadsom – May’s 2016 leadership rival – who has moved on to become leader of the House of Commons.
Gove's new role in charge of Defra gives him the difficult tasks of ensuring all relevant EU regulations are transposed into UK law following Brexit, and of releasing the much-delayed 25-Year Plan for the environment.
His return was the only big surprise in the reshuffle.
The roles of junior Defra ministers - farming minister George Eustice, Therese Coffey and Lord Gardiner - remain unchanged. Andrew Percy remains parks minister at DCLG.
HTA horticulture head Raoul Curtis-Machin said: "We look forward to finding out more about his plans next month when we have an APPGHG Ministerial meeting booked for 5 July. We hope he will bring energy and enthusiasm to our Sector Deal discussion."
British Growers Association chief executive Jack Ward said: "Michael Gove comes with a reputation of being quite outspoken. For food and farming, that could be a good thing, if he's prepared to represent the sector in the right way."
And while Gove is known as a Brexit supporter and advocate of free trade with the wider world, "the whole substance of that debate has changed" since Thursday's General Election, Ward added.
"With a majority the government could push through what it wanted but now it will have to take a much more conciliatory approach, and avoid any cliff edges."
NFU president Meurig Raymond responded with an open letter to Gove MP demanding a post-Brexit trade deal to deliver access to the EU market and workforce, and for the re-authorisation of glyphosate.
"With farming arguably the sector most impacted by Brexit, NFU members need certainty as soon as possible that this Government will make Brexit a success for British food and farming," the letter said.
"To achieve our potential, we need a future post-Brexit trade arrangement that delivers the best possible access to the vital EU market, as well as continued access to a competent and reliable workforce."
It added: "Licensing and access to plant protection products is another area of concern for UK farmers; the NFU has consistently advocated for regulation to be based on robust, scientific evidence and consequently I very much hope you will be able to give your support to the reauthorisation of glyphosate which is a very important product for British farmers to have access to."