Few predicted a happy ending: "A deal for destruction", "Strange bedfellows", and "Waterstones let the fox into the chicken run" exclaimed some of the resulting headlines.
Had the former JP Morgan banker doomed the group less than a year after being appointed as its managing director?
"A world that is totally dominated by Amazon will be a poorer one," Mr Daunt tells the BBC when asked about the decision.
"But that is not to say that I don't think that Amazon is - within the limits of what it does - absolutely fantastic."
Secret deal The 49-year-old has already distanced Waterstones from its roots, dropping the apostrophe in its name to the dismay of punctuation campaigners. But the decision to ditch Sony's e-readers and promote Amazon's is clearly his most controversial to date.
For someone who has apparently signed his company's death warrant he appears focused and optimistic about the group's future, determined to complete a costly refit programme designed to upgrade its 300 stores.
And though he remains tight-lipped about the terms of the Amazon arrangement, he insists the agreement is to his advantage, whatever others suggest.
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