Thank you Kevin.
I performed
rm -fr /var/www/.gnupg
and then
sudo su -s /bin/bash -c "gpg2 --import /var/www/passbolt_api/config/gpg/serverkey_private.asc" www-data
now if I look at the keys I see
mzanetti@localhost:~$ sudo su -s /bin/bash -c "gpg2 --list-keys --fingerprint" www-data
/var/www/.gnupg/pubring.kbx
---------------------------
pub   rsa2048/5335C8B5 2018-07-18 [SC]
      Key fingerprint = EB8D CF29 1ED1 E680 91E3  8F69 A6DA 4E2D 5335 C8B5
uid         [ unknown] company Testing (company Testing key) <company.testing@gmail.com>
sub   rsa2048/F23A5957 2018-07-18 [E]
mzanetti@localhost:~$ sudo su -s /bin/bash -c "gpg2 --list-secret-keys --fingerprint" www-data
/var/www/.gnupg/pubring.kbx
---------------------------
sec   rsa2048/5335C8B5 2018-07-18 [SC]
      Key fingerprint = EB8D CF29 1ED1 E680 91E3  8F69 A6DA 4E2D 5335 C8B5
uid         [ unknown] company Testing (company Testing key) <company.testing@gmail.com>
ssb   rsa2048/F23A5957 2018-07-18 [E]
It looks all VERY fine to me. The keys are the same, I just have one issue…

The error is always there!!! -.-