Introduced in the Season Five episode A Little Bit Stronger, Daphne learns from her friend Louisa that he likes Daphne and wants her phone number. However, Daphne does not know how to act around him but eventually asks him if he wants her number.
When Maddie finds out the truth about the nasty GIFs online in the episode Not Ready to Make Nice, Deacon confiscates Daphne's phone, where she misses a phone call from Flynn, but he later calls Maddie's phone with the latter telling Deacon that she and Daphne made up with each other and she said that Daphne could use her phone.
Following Rayna's car crash, Daphne is called away from choir practice and refuses to attend the talent show as it means leaving her mother but Flynn arranges for the choir to show up at the hospital.
In the second episode of the final season, he and Daphne notice Jake Maitland standing by a tree acting strangely and she latter decides not to sit with Flynn while having lunch, opting to talk to Jake instead.