In our firms Jira instance, we have to use a personal certificate (PKCS#12) in order to open the page. After I am authenticated the page is shown where I can now interface with Jira such as logging into it with my regular username and password. 

Currently this is not possible using Jira plugin or any Jira plugin for that matter. The Jenkns server that I am using this on is a Windows machine. I've tried installing the personal certificate in that server in the service account that the Jenkins service is running as. I also tried adding the personal certificate in the JRE's certificate store (cacert). Albeit, I had to convert it first. I also tested that I can access Jira using the browser in the Jenkins server logged in as the Jenkins service account.

In the Jenkins Configuration Jira plugin settings, when I try to validate the settings, I get the following exception stack (note I've obfuscated irrelevant text):

Caused by: org.apache.http.ProtocolException: Not a valid protocol version: You are not allowed to access this resource. For support please email: xxx@xxxxxx.com or call (xxx) xxx-xxxx Caused by: org.apache.http.ProtocolException: Not a valid protocol version: You are not allowed to access this resource. For support please email: xxx@xxxx.com or call (xxx) xxx-xxxx at org.apache.http.impl.nio.codecs.AbstractMessageParser.parse(AbstractMessageParser.java:209) at org.apache.http.impl.nio.DefaultNHttpClientConnection.consumeInput(DefaultNHttpClientConnection.java:245) at org.apache.http.impl.nio.client.InternalIODispatch.onInputReady(InternalIODispatch.java:81) at org.apache.http.impl.nio.client.InternalIODispatch.onInputReady(InternalIODispatch.java:39) at org.apache.http.impl.nio.reactor.AbstractIODispatch.inputReady(AbstractIODispatch.java:121) at org.apache.http.impl.nio.reactor.BaseIOReactor.readable(BaseIOReactor.java:162) at org.apache.http.impl.nio.reactor.AbstractIOReactor.processEvent(AbstractIOReactor.java:337) at org.apache.http.impl.nio.reactor.AbstractIOReactor.processEvents(AbstractIOReactor.java:315) at org.apache.http.impl.nio.reactor.AbstractIOReactor.execute(AbstractIOReactor.java:276) at org.apache.http.impl.nio.reactor.BaseIOReactor.execute(BaseIOReactor.java:104) at org.apache.http.impl.nio.reactor.AbstractMultiworkerIOReactor$Worker.run(AbstractMultiworkerIOReactor.java:588)