With HestiaCP, you can install letsencrypt SSL but if your site is behind Cloudflare proxy, SSL from Cloudflare. Here is a step-by-step guide how to use the free certificate from Cloudflare.
After setting up the domain at hestiaCP panel, there is an option Enable SSL for this domain

Click at Enable SSL for this domain and this will open the bellow options

Now you should go to Cloudflare and click at SSL/TTL Tab
You should also refer to https://docs.hestiacp.com/admin_docs/ssl_certificates.html#can-i-use-a-cloudflare-origin-ssl-certificate-with-cloudflare

This will show you

And click Origin Server and Create Certificate (The blue button)
Next this will pop-up a window with the domain you want to add SSL certificate, years etc

This will create the certificate and will be like this (Origin Certificate and Private key), don’t close this window, first copy both codes
Back to HestiaCP copy and paste the above code

At SSL Certificate Authority/ Intermediate (Optional), you must put the code from Cloudflare Origin CA
-----BEGIN CERTIFICATE----- MIID/DCCAuagAwIBAgIID+rOSdTGfGcwCwYJKoZIhvcNAQELMIGLMQswCQYDVQQG EwJVUzEZMBcGA1UEChMQQ2xvdWRGbGFyZSwgSW5jLjE0MDIGA1UECxMrQ2xvdWRG bGFyZSBPcmlnaW4gU1NMIENlcnRpZmljYXRlIEF1dGhvcml0eTEWMBQGA1UEBxMN U2FuIEZyYW5jaXNjbzETMBEGA1UECBMKQ2FsaWZvcm5pYTAeFw0xNDExMTMyMDM4 NTBaFw0xOTExMTQwMTQzNTBaMIGLMQswCQYDVQQGEwJVUzEZMBcGA1UEChMQQ2xv dWRGbGFyZSwgSW5jLjE0MDIGA1UECxMrQ2xvdWRGbGFyZSBPcmlnaW4gU1NMIENl cnRpZmljYXRlIEF1dGhvcml0eTEWMBQGA1UEBxMNU2FuIEZyYW5jaXNjbzETMBEG A1UECBMKQ2FsaWZvcm5pYTCCASIwDQYJKoZIhvcNAQEBBQADggEPADCCAQoCggEB AMBIlWf1KEKR5hbB75OYrAcUXobpD/AxvSYRXr91mbRu+lqE7YbyyRUShQh15lem ef+umeEtPZoLFLhcLyczJxOhI+siLGDQm/a/UDkWvAXYa5DZ+pHU5ct5nZ8pGzqJ p8G1Hy5RMVYDXZT9F6EaHjMG0OOffH6Ih25TtgfyyrjXycwDH0u6GXt+G/rywcqz /9W4Aki3XNQMUHNQAtBLEEIYHMkyTYJxuL2tXO6ID5cCsoWw8meHufTeZW2DyUpl yP3AHt4149RQSyWZMJ6AyntL9d8Xhfpxd9rJkh9Kge2iV9rQTFuE1rRT5s7OSJcK xUsklgHcGHYMcNfNMilNHb8CAwEAAaNmMGQwDgYDVR0PAQH/BAQDAgAGMBIGA1Ud EwEB/wQIMAYBAf8CAQIwHQYDVR0OBBYEFCToU1ddfDRAh6nrlNu64RZ4/CmkMB8G A1UdIwQYMBaAFCToU1ddfDRAh6nrlNu64RZ4/CmkMAsGCSqGSIb3DQEBCwOCAQEA cQDBVAoRrhhsGegsSFsv1w8v27zzHKaJNv6ffLGIRvXK8VKKK0gKXh2zQtN9SnaD gYNe7Pr4C3I8ooYKRJJWLsmEHdGdnYYmj0OJfGrfQf6MLIc/11bQhLepZTxdhFYh QGgDl6gRmb8aDwk7Q92BPvek5nMzaWlP82ixavvYI+okoSY8pwdcVKobx6rWzMWz ZEC9M6H3F0dDYE23XcCFIdgNSAmmGyXPBstOe0aAJXwJTxOEPn36VWr0PKIQJy5Y 4o1wpMpqCOIwWc8J9REV/REzN6Z1LXImdUgXIXOwrz56gKUJzPejtBQyIGj0mveX Fu6q54beR89jDc+oABmOgg== -----END CERTIFICATE-----
Now click Save, and SSL must be enabled
You should also refer to SSL Certificates and Let’s Encrypt from HestiaCP