Put simply, he could not live in his hometown because of his Christianity, and he could not live in Lagos because of the prevalence of Covid-19 there.
The Government appealed the tribunal's decision and argued that the man could have been sent to any other city in Nigeria and avoided harm from his family and from the virus.
The Auckland High Court this year denied that appeal on the grounds that the Immigration and Protection Tribunal had made the right call in letting the man stay.
The Crown argued that the tribunal didn't even look at other Nigerian cities other than Lagos when considering whether it was safe for the man to return home.
"It did not go on to assess whether other parts of Nigeria might be safe for the respondent: it simply granted him refugee status," it said in submissions to the court.
"Eliminating Lagos city as a viable internal protection alternative did not justify the further conclusion that protection was unavailable in Nigeria as a whole."
The tribunal last year found that Lagos would have been safe for the man in a religious sense, but not in a health sense.
"The chance of somebody who knew his father walking along the street at the same time as him, including when he was ministering in the street, or while he was volunteering, and recognising him as being his father's apostate Christian son is random, remote and well below the real chance threshold," it said.
"What is certain, however, is that given his heightened vulnerability should he contract Covid-19 in Lagos at a time of systemic stress on the healthcare system, the consequences for him could be dire, if not fatal."
Despite the Crown arguing that other Nigerian cities would be a viable option for the man, Justice Mark Woolford said at the time of the tribunal's decision all of Nigeria was suffering badly from the pandemic.
"The Covid-19 pandemic does not respect international or internal boundaries," he said.
"Although rates of infection have varied between the various Nigerian states, all states have been affected."
Justice Woolford said the tribunal had not erred when granting the man protected refugee status and overturned the Crown's appeal.