The decision backs the recommendation of a planning inspector.
Applicants and landowners Mr and Mrs S Andrews appealed after Cornwall Council refused retrospective permission for the 20KW wind turbines.
The scheme, near the town of Fowey, would have generated electricity for their farm and connect to the National Grid, according to a letter sent on behalf of Pickles.
The report by inspector Neil Pope said that the site forms part of the South Coast – Eastern Section of the Cornwall Area of Outstanding Natural Beauty.
A Grade I listed church, the Castle Dore Scheduled Ancient Monument and the site of the 1644 Battle of Lostwithiel are all within 1.5 km of the site, with further Grade II listed buildings nearby.
In reaching his decision, Pickles’ letter stated that he gave "substantial weight" to the economic and environmental benefits of the scheme, but found that it harms the "scenic qualities and natural beauty" of the AONB, something he attached "great weight" to.
He also, the letter said, believed it would harm the listed buildings and ancient monument. "He gives considerable importance and weight to the desirability of preserving the historic assets", it added.
The scheme further conflicts with policies in the emerging Cornwall Local Plan, Pickles found.
Compass reference: 200-003-056