The couple, who married in 2015 and share two children, announced their split in early September.
But according to official divorce documents obtained by Entertainment Tonight, Deschanel and Pechenik have been separated since January.
In the documents, Pechenik reportedly cites “irreconcilable differences” as the reason for the divorce and has asked for joint legal and physical custody of the couple’s children, Elsie, four, and Charlie, two.
At the time of their split, the couple issued a joint statement explaining they would continue to remain close.
“After much discussion and a long period of contemplation we have decided we are better off as friends, business partners and co-parents rather than life partners,” the joint statement read.
“We remain committed to our business, our values, and most of all, our children. Thank you for respecting our privacy at this time.”
Prior to their split, the couple founded The Farm Project, an initiative that aims to help connect farmers to consumers and encourage people to think about where they source their food.
“We want to make it easy for everyone to grow food themselves and connect directly with farmers in their communities,” its website reads.
“We aim to empower people to ask the right questions – because when we ask the right questions, we can make informed choices and vote with our dollars for a better food system.”