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You might like P.C.Doherty's Hugh Corbett series - Corbett is an agent of Edward I of England.
A bit later than medieval - there is a series by S.J.Parris about Giordano Bruno investigating murders in Elizabethan England.
Not strictly murder mystery (but lots of plotting and skullduggery), there is "Cathedral of the Sea" by Ildefonso Falcones, set in 1300's Barcelona.
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