Catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides, such as Leu-Pro-Ala. Also shows low activity towards peptides with Ala or Ser at the P1 position. Release of any N-terminal amino acid, including proline, that is linked to proline, even from a dipeptide or tripeptide. Binds 2 manganese ions per subunit. Homodimer. Mainly mitochondrial. Belongs to the peptidase M24B family.