You can also use a hardware token to handle the encryption/decryption (yubikey/nitrokey/GnuPG smartcard/...).
If you have a trojan on your computer it'll still be able to decrypt your passwords while the token is plugged and unlocked of course, but at least offline attacks shouldn't be possible. Of course that doesn't mean you shouldn't use 2FA wherever possible to mitigate the risks further.
Some tokens can also be configured to wait for a physical button press to allow the decryption which which can help prevent a complete background decryption of your passwords (assuming that each password is stored with a different key, like with password-store for instance).
If you have a trojan on your computer it'll still be able to decrypt your passwords while the token is plugged and unlocked of course, but at least offline attacks shouldn't be possible. Of course that doesn't mean you shouldn't use 2FA wherever possible to mitigate the risks further.
Some tokens can also be configured to wait for a physical button press to allow the decryption which which can help prevent a complete background decryption of your passwords (assuming that each password is stored with a different key, like with password-store for instance).