Prester John was actually a character that comes from long before Polo, The story goes that the first reports of Prester John comes from the reports of a menacing force ripping through Muslim lands and killing all he saw. This man, of course, was not a Christian priest-King, but Genghis Khan. The Pope even received a letter from ‘Prester John’ around this period, but either the Pope made this up or his letter was forged by someone else. Not knowing of Mongolia, of course, it was presumed that his kingdom was in India, which made much later Portuguese expeditions to India rather confusing.

The association with Ethiopia comes from much later, in the 1500’s. Originally, there were 4 Christian kingdoms in NE Africa. However, they eventually all got gobbled up, leaving Ethiopia (or Abyssinia) as the sole Christian presence in the area. When the Portuguese were doing the rounds around Africa, they found a devout Christian kingdom in the middle of nowhere. As such, they presumed it was Prester John, coming to save Christianity at last. Alas, it was a fractured feudal mess, at risk of being swallowed up by the Islamic Adal. So, Portugal ended up helping them instead.

Sources-

Silk Roads- A new History of the World

The Penguin Atlas of African History