St Theodore was constructed in the mid 16th century and used to be a small one nave edifice which is now connected with the larger new church.
During the uncertain first decade of the 19th century it was destroyed by Ottoman bandits called kardzhalii and restored between 1808 and 1809 by orders of the Bishop of Plovdiv Dionisius.
The construction of the Church of the Holy Mother of God started in 1818 near the southern wall of the old building and was finished in 1823.
The edifice was constructed by craftsmen from Bratsigovo while the interior was decorated by painters from the famous Samokov school.
The interior was badly damaged when the Ottomans burned Panagyurishte during the April Uprising in 1876.