The three watercolours by artist Cliff Wright were being sold at Christie's.
Beforehand, the Christie's book illustration specialist, was "excited" about a fierce bidding battle.
Hayden Pyle said: "In terms of Harry Potter book covers, only one has come up for sale so far.
"That was the cover of the first book, which made more than £85,000."
But in the end, he was proved wrong, and the cover remained unsold.
The two paintings which did sell went to an antique booksellers in London - who is expected to sell them on to a British collector.