I'm experiencing exactly same issue. I'm adding jobs via Blueocean UI which creates "Pipeline Multibranch" jobs. And I don't see webhooks configured, even after initial manual build.

Once I go to "Manage Jenkins > Configure System > GitHub plugin > Advanced > Re-register hooks for all jobs"  Webhooks get created.

How this can  be solved? What I'm doing wrong?

Alex Simenduev this is a bug somehow (a regression). 

After a lot of debugging, It seems like the webhooks aren't registered until a branch is built once because the existing GitHubRepositoryNameContributor implementations needs some information attached during the build to determine what repo to add the webhook to.
There is no specific GitHubRepositoryNameContributor implemented for GitHub branch source that can extract that information ahead of the build.

Still confused how this ever worked: surely an older version of GHBS worked out of the box without requiring a build first (seems a chicken and egg problem - it needs webhooks to trigger a build, although should there be a first time build and THEN try to setup the webhooks not up front?)

Code changed in jenkins
User: rsandell
Path:
pom.xml
src/main/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceRepositoryNameContributor.java
http://jenkins-ci.org/commit/github-branch-source-plugin/9213e3b0d1b12493e5d319fb4f3cb0f7be05edac
Log:
JENKINS-48035 Add a GitHubRepositoryNameContributor that recognises multi branch

The existing name contributors could only find the repo name if a build
of a branch had been made and added git build data to the job.
Since branches are discovered and built after GitHubSCMSource.afterSaved is called
there was no repo names recognised to add webhooks to.

This only solves the case when a single multi branch project is created.
Because when an org folder creates the multi branch jobs it does not call
afterSaved on the children. So that needs to be fixed someplace else.

Code changed in jenkins
User: rsandell
Path:
pom.xml
src/main/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceRepositoryNameContributor.java
http://jenkins-ci.org/commit/github-branch-source-plugin/93cc3f46474d74a9b7defa7c43ab3c1a59c87a04
Log:
JENKINS-48035 Revert branch-api back to test scope and use SCMSourceOwner

Code changed in jenkins
User: rsandell
Path:
src/test/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceTest.java
http://jenkins-ci.org/commit/github-branch-source-plugin/945bd9842f98446123c4156fcf23962eabbc3b11
Log:
JENKINS-48035 Add a test

Code changed in jenkins
User: rsandell
Path:
src/main/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceRepositoryNameContributor.java
http://jenkins-ci.org/commit/github-branch-source-plugin/361e6d15eb71466e67081333bdfd7ab0da08b082
Log:
JENKINS-48035 And the license header

Code changed in jenkins
User: rsandell
Path:
src/test/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceTest.java
http://jenkins-ci.org/commit/github-branch-source-plugin/0203fb201fc886ac826c96386f88b3d7775ab8f1
Log:
JENKINS-48035 negative tests

Code changed in jenkins
User: rsandell
Path:
src/main/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceRepositoryNameContributor.java
http://jenkins-ci.org/commit/github-branch-source-plugin/99d72b0ae93952b5fb941d6f71f63d45abf7cab2
Log:
JENKINS-48035 javadoc

Code changed in jenkins
User: Stephen Connolly
Path:
pom.xml
src/main/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceRepositoryNameContributor.java
src/test/java/org/jenkinsci/plugins/github_branch_source/GitHubSCMSourceTest.java
http://jenkins-ci.org/commit/github-branch-source-plugin/3bf8714bffc7467d81099542e3e421203a4695a0
Log:
Merge pull request #170 from rsandell/JENKINS-48035

JENKINS-48035 Add a GitHubRepositoryNameContributor that recognises…

Compare: https://github.com/jenkinsci/github-branch-source-plugin/compare/267e41c59581...3bf8714bffc7

claimed resolved in 2.3.2

Just reopening to make sure we do org folders as well 

Stephen Connolly can this then be closed? 

rsandell Stephen Connolly I am reopening this ticket again because the same reported issue seems to be back running (Regression?)

Environment

Jenkins LTS 2.164.2
 * github:1.29.4 'GitHub plugin'
 * github-api:1.95 'GitHub API Plugin'
 * github-branch-source:2.5.0 *(update available)* 'GitHub Branch Source Plugin'

Observations

What we see on Jenkins logs

May 16, 2019 3:12:38 PM org.jenkinsci.plugins.github.webhook.WebhookManager$2 applyNullSafe
WARNING: Failed to add GitHub webhook for GitHubRepositoryName[host=github.com,username=mock-carlosrodlop-org,repository=my-hw-maven-app]
java.lang.NullPointerException: There are no credentials with admin access to manage hooks on GitHubRepositoryName[host=github.com,username=mock-carlosrodlop-org,repository=my-hw-maven-app]

But it is not right... I am using this repo https://github.com/mock-carlosrodlop-org/my-hw-maven-app with user:carlosrodlop and pass:APIToken and as you can tell from the following images carlosrodlop is an admin

Custom dedicated loggers as explained in this guide: GitHub-Webhook-Troubleshooting are not providing any useful hint just

May 16, 2019 4:05:50 PM FINE com.cloudbees.jenkins.GitHubWebHook$1 apply
Calling registerHooks() for multibranch-example-job
May 16, 2019 4:05:51 PM FINE com.cloudbees.jenkins.GitHubWebHook$1 apply
Calling registerHooks() for multibranch-example-job

Manage Jenkins > GitHub plugin > Advanced > Re-register hooks for all jobs > webhook in GitHub is NOT generated either. Independently if I enabled or disable Manage hooks options the output is the same: Works only when Jenkins manages hooks (one or more creds specified)

It is working fine after deep testing

Carlos Rodríguez López I experienced the same issue you did. What do you mean "It is working fine after deep testing"? How did your problem disappear?

While my OAuth token used by Jenkins has the admin:repo_hook permission on Github, Jenkins throws this exception for all of my managed repositories:

Jul 06, 2019 10:34:16 AM WARNING org.jenkinsci.plugins.github.webhook.WebhookManager$2 applyNullSafe
Failed to add GitHub webhook for GitHubRepositoryName[host=github.com,username=*****,repository=*****]
java.lang.NullPointerException: There are no credentials with admin access to manage hooks on GitHubRepositoryName[host=github.com,username=*****,repository=*****]
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:231)
at org.jenkinsci.plugins.github.webhook.WebhookManager$2.applyNullSafe(WebhookManager.java:179)
at org.jenkinsci.plugins.github.webhook.WebhookManager$2.applyNullSafe(WebhookManager.java:175)
at org.jenkinsci.plugins.github.util.misc.NullSafeFunction.apply(NullSafeFunction.java:18)
at com.google.common.collect.Iterators$8.next(Iterators.java:812)
at com.google.common.collect.Iterators$7.computeNext(Iterators.java:648)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at com.google.common.collect.Iterators$7.computeNext(Iterators.java:647)
at com.google.common.collect.AbstractIterator.tryToComputeNext(AbstractIterator.java:143)
at com.google.common.collect.AbstractIterator.hasNext(AbstractIterator.java:138)
at com.google.common.collect.Lists.newArrayList(Lists.java:138)
at com.google.common.collect.Lists.newArrayList(Lists.java:119)
at org.jenkinsci.plugins.github.util.FluentIterableWrapper.toList(FluentIterableWrapper.java:147)
at org.jenkinsci.plugins.github.webhook.WebhookManager$1.run(WebhookManager.java:127)
at hudson.util.SequentialExecutionQueue$QueueEntry.run(SequentialExecutionQueue.java:119)
at jenkins.util.ContextResettingExecutorService$1.run(ContextResettingExecutorService.java:28)
at jenkins.security.ImpersonatingExecutorService$1.run(ImpersonatingExecutorService.java:59)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

FYI I fixed my issue by regenerating my OAuth access token. It may have been misconfigured in my Jenkins' credentials...

Hi David Lakatos,

I forgot to configure correctly the Git Plugin see https://support.cloudbees.com/hc/en-us/articles/224543927-GitHub-Integration-Webhooks

Regards,