I installed Lets Encrypt plugin in my WHM and run for one of my site but it when I'm checking to sslshopper site to confirm that certificate is installed or not it shows :

Common name: example.io
SANs: example.io, cpanel.example.io, mail.example.io, webdisk.example.io, webmail.example.io, www.example.io
Valid from December 25, 2018 to March 26, 2019
Serial Number: 3471bd46e8f1080f957b391a3cd9c655
Signature Algorithm: sha256WithRSAEncryption
Issuer: cPanel, Inc. Certification Authority

Common name: cPanel, Inc. Certification Authority
Organization: cPanel, Inc.
Location: Houston, TX, US
Valid from May 17, 2015 to May 17, 2025
Serial Number: f01d4bee7b7ca37b3c0566ac05972458
Signature Algorithm: sha384WithRSAEncryption
Issuer: COMODO RSA Certification Authority  

Common name: COMODO RSA Certification Authority
Organization: COMODO CA Limited
Location: Salford, Greater Manchester, GB
Valid from May 30, 2000 to May 30, 2020
Serial Number: 2766ee56eb49f38eabd770a2fc84de22
Signature Algorithm: sha384WithRSAEncryption
Issuer: AddTrust External CA Root

So I'm confused if Letsencrypt is installed or not

closed as off-topic by Iain, womble Dec 27 '18 at 10:55

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I'd say the checked site is not using a Let's Encrypt certificate: it should show Let's Encrypt as the first Issuer:.

I use this command to check a website:

openssl s_client -servername example.io -connect example.io:443 </dev/null

If the certificate is issued by Let's Encrypt, I would expect to find this in the output:

Certificate chain
 0 s:/CN=example.io
   i:/C=US/O=Let's Encrypt/CN=Let's Encrypt Authority X3
 1 s:/C=US/O=Let's Encrypt/CN=Let's Encrypt Authority X3
   i:/O=Digital Signature Trust Co./CN=DST Root CA X3

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