Their appeal decision is expected within 20 days.
Yaser Mosibzadeh, Saheb Fadayee and Mohammad Reza Omidi were arrested at their house church in Rasht on 13 May 2016 as they were celebrating communion. They were charged with acting against national security.
In 2012, Omidi was flogged for the same crime.
Anti-persecution charity Release International is calling on the Iranian government to rethink the punishment.
"How can it be right to be whipped for taking communion wine?" said Paul Robinson, chief executive of Release International.
"The right thing to do would be to overturn this unjust sentence. Release hopes this will pave the way for long-awaited religious freedom in Iran."
The men are all Muslim converts to Christianity. The sentence reflects the state's refusal to recognise the right for Muslims to convert to other religions.
"These charges reflect the state position that once a Muslim, always a Muslim," Paul Robinson added. "Behind this case is the denial of that most fundamental right - the right to choose your own religion without state interference."
Iran stepped up its crackdown on Christian activists in 2015. Around 90 prisoners are now in jail for their faith. According to Release International, many have been beaten and abused.