Were any of the films made over the years about the Tudors ever filmed at the actual spots? If so do they have to get Queen Elizabeth’s permission to shoot in the actual locations?

Filming locations for the first Elizabeth film starring Cate Blanchett included:-
Alnwick Castle, Northumberland
Aydon Castle, Northumberland
Bamburgh Castle, Northumberland
Bolton Castle, North Yorkshire
Durham Cathedral, County Durham
Haddon Hall, Derbyshire
Leeds Castle, Kent
Middle Temple, Holborn, London
Raby Castle, Durham
York Minster, York

Elizabeth the Golden Age film locations included
Baddesley Clinton, Warwickshire
Brean Down, Somerset (stood in for Tilbury)
Burghley House, Lincolnshire
Dorney Court, Buckinghamshire
Doune Castle, Stirling, Scotland
Eilean Donan Castle, Scotland
Ely Cathedral, Ely
Hatfield House, Herts
Leeds Castle, Kent
Petworth House, Sussex
St John's College, Cambridge
Wells Cathedral, Somerset
Westminster Cathedral, London
Winchester Cathedral, Winchester

So, yes, some real historical spots were used although generally as stand-ins for places which do not stand today: Ely Cathedral stood in for the interior of Whitehall, Leeds Castle for Whitehall and Chartley Hall, St Bartholomew's Hospital in London was used as Fotheringhay and Winchester Cathedral stood in for the old St Paul's Cathedral.
Permission would have been needed from the trusts which own the different properties, e.g. English Heritage, National Trust, the Church of England and private owners/companies.

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