You can use SQLite's function creation routines (PHP manual):
$db_obj->sqliteCreateFunction('Encrypt', 'MyEncryptFunction', 2);
$db_obj->sqliteCreateFunction('Decrypt', 'MyDecryptFunction', 2);
When inserting data, you can use the encryption function directly and INSERT the encrypted data or you can use the custom function and pass unencrypted data:
$insert_obj = $db_obj->prepare('INSERT INTO table (Clear, Encrypted) ' .
'VALUES (:clear, Encrypt(:data, "' . $passwordhash_str . '"))');
When retrieving data, you can also use SQL search functionality:
$select_obj = $db_obj->prepare('SELECT Clear, ' .
'Decrypt(Encrypted, "' . $passwordhash_str . '") AS PlainText FROM table ' .
'WHERE PlainText LIKE :searchterm');