Do you mean with words that are spelt the same way in the religious texts as well as in Modern Greek? In that case, there are some differences. For example, in the church pronunciation, the various ways of spelling the sound are always pronounced as a full vowel, which may not be the case in the modern language when they occur before another vowel -- á¼€Î»Î®Î¸ÎµÎ¹Î± will have 4 syllables in church but has 3 in modern Greek. Another thing is that in combinations like Î¼Ï€, Î½Ï„, Î³Îº, Î³Î³, the first letter is always pronounced in church, while it may or may not be in the modern language -- Ï€ÎÎ½Ï„Îµ is always [pende] in church, but can be [pede] in everyday life.
On second thought, it's not really a different pronunciation -- the actual values given to letters are the same. It's not as if Ï… and Î¿Î¹ were pronounced like French u, for example.