We can encrypt each section of the web.config using the encryption provided by aspnet_regiis.exe.
Encrypt Connection String
C:\WebPortal>aspnet_regiis.exe -pef connectionStrings c:\WebPortal-prov
"RsaProtectedConfigurationProvider"
Encrypting configuration section.
Succeeded!
Here the -pe switch specifies the configuration section "connectionStrings" to encrypt.
C:\WebPortal>aspnet_regiis.exe -pdf connectionStrings c:\WebPortal
Decrypting configuration section.
Succeeded!
Here the -pef switch specifies the configuration section to encrypt and allows you to supply the physical directory path for your configuration file.
Encrypt AppSettings
C:\WebPortal>aspnet_regiis.exe -pef appSettings c:\WebPortal-prov "RsaProtectedConfigurationProvider"
Encrypting configuration section.
Succeeded!
Here the -prov switch specifies the provider name.
C:\WebPortal>aspnet_regiis.exe -pdf appSettings c:\WebPortal
Decrypting configuration section.
Succeeded!