diff --git a/.ci/check-changelogs.groovy b/.ci/check-changelogs.groovy
index a1523c83fbb..6185160784a 100644
--- a/.ci/check-changelogs.groovy
+++ b/.ci/check-changelogs.groovy
@@ -49,7 +49,7 @@ pipeline {
         deleteDir()
         unstash 'source'
         dir("${BASE_DIR}"){
-          sh(label: 'Run check changelogs', script: './script/jenkins/check-changelogs.sh')
+          sh(label: 'Run check changelogs', script: './.ci/scripts/check-changelogs.sh')
         }
       }
     }
diff --git a/script/jenkins/bench.sh b/.ci/scripts/bench.sh
similarity index 100%
rename from script/jenkins/bench.sh
rename to .ci/scripts/bench.sh
diff --git a/.ci/scripts/build-darwin.sh b/.ci/scripts/build-darwin.sh
index b7625f8a684..4a2f561b5bd 100755
--- a/.ci/scripts/build-darwin.sh
+++ b/.ci/scripts/build-darwin.sh
@@ -6,4 +6,4 @@ source ./script/common.bash
 
 jenkins_setup
 
-./script/jenkins/build.sh
+./.ci/scripts/build.sh
diff --git a/script/jenkins/build.sh b/.ci/scripts/build.sh
similarity index 100%
rename from script/jenkins/build.sh
rename to .ci/scripts/build.sh
diff --git a/script/jenkins/check-changelogs.sh b/.ci/scripts/check-changelogs.sh
similarity index 100%
rename from script/jenkins/check-changelogs.sh
rename to .ci/scripts/check-changelogs.sh
diff --git a/script/jenkins/intake.sh b/.ci/scripts/intake.sh
similarity index 100%
rename from script/jenkins/intake.sh
rename to .ci/scripts/intake.sh
diff --git a/script/jenkins/linux-test.sh b/.ci/scripts/linux-test.sh
similarity index 100%
rename from script/jenkins/linux-test.sh
rename to .ci/scripts/linux-test.sh
diff --git a/script/jenkins/package-docker-snapshot.sh b/.ci/scripts/package-docker-snapshot.sh
similarity index 100%
rename from script/jenkins/package-docker-snapshot.sh
rename to .ci/scripts/package-docker-snapshot.sh
diff --git a/script/jenkins/package.sh b/.ci/scripts/package.sh
similarity index 100%
rename from script/jenkins/package.sh
rename to .ci/scripts/package.sh
diff --git a/script/jenkins/sync.sh b/.ci/scripts/sync.sh
similarity index 100%
rename from script/jenkins/sync.sh
rename to .ci/scripts/sync.sh
diff --git a/.ci/scripts/test-darwin.sh b/.ci/scripts/test-darwin.sh
index aa671118644..6df42b0ba72 100755
--- a/.ci/scripts/test-darwin.sh
+++ b/.ci/scripts/test-darwin.sh
@@ -17,4 +17,4 @@ source ./script/common.bash
 
 jenkins_setup
 
-script/jenkins/unit-test.sh
+./.ci/scripts/unit-test.sh
diff --git a/script/jenkins/test-install-packages.sh b/.ci/scripts/test-install-packages.sh
similarity index 100%
rename from script/jenkins/test-install-packages.sh
rename to .ci/scripts/test-install-packages.sh
diff --git a/script/jenkins/unit-test.sh b/.ci/scripts/unit-test.sh
similarity index 100%
rename from script/jenkins/unit-test.sh
rename to .ci/scripts/unit-test.sh
diff --git a/script/jenkins/windows-build.ps1 b/.ci/scripts/windows-build.ps1
similarity index 100%
rename from script/jenkins/windows-build.ps1
rename to .ci/scripts/windows-build.ps1
diff --git a/script/jenkins/windows-test.ps1 b/.ci/scripts/windows-test.ps1
similarity index 100%
rename from script/jenkins/windows-test.ps1
rename to .ci/scripts/windows-test.ps1
diff --git a/Jenkinsfile b/Jenkinsfile
index 1294ef05466..3ec9ef99513 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -112,7 +112,7 @@ pipeline {
           deleteDir()
           unstash 'source'
           dir("${BASE_DIR}"){
-            sh(label: 'Run intake', script: './script/jenkins/intake.sh')
+            sh(label: 'Run intake', script: './.ci/scripts/intake.sh')
           }
         }
       }
@@ -140,7 +140,7 @@ pipeline {
                 dir(BASE_DIR){
                   retry(2) { // Retry in case there are any errors to avoid temporary glitches
                     sleep randomNumber(min: 5, max: 10)
-                    sh(label: 'Linux build', script: './script/jenkins/build.sh')
+                    sh(label: 'Linux build', script: './.ci/scripts/build.sh')
                   }
                 }
               }
@@ -170,8 +170,8 @@ pipeline {
               dir(BASE_DIR){
                 retry(2) { // Retry in case there are any errors to avoid temporary glitches
                   sleep randomNumber(min: 5, max: 10)
-                  powershell(label: 'Windows build', script: '.\\script\\jenkins\\windows-build.ps1')
-                  powershell(label: 'Run Window tests', script: '.\\script\\jenkins\\windows-test.ps1')
+                  powershell(label: 'Windows build', script: '.\\.ci\\scripts\\windows-build.ps1')
+                  powershell(label: 'Run Window tests', script: '.\\.ci\\scripts\\windows-test.ps1')
                 }
               }
             }
@@ -245,7 +245,7 @@ pipeline {
               deleteDir()
               unstash 'source'
               dir("${BASE_DIR}"){
-                sh(label: 'Run Unit tests', script: './script/jenkins/unit-test.sh')
+                sh(label: 'Run Unit tests', script: './.ci/scripts/unit-test.sh')
               }
             }
           }
@@ -287,7 +287,7 @@ pipeline {
               deleteDir()
               unstash 'source'
               dir("${BASE_DIR}"){
-                sh(label: 'Run Linux tests', script: './script/jenkins/linux-test.sh')
+                sh(label: 'Run Linux tests', script: './.ci/scripts/linux-test.sh')
               }
             }
           }
@@ -335,7 +335,7 @@ pipeline {
               unstash 'source'
               golang(){
                 dir("${BASE_DIR}"){
-                  sh(label: 'Run benchmarks', script: './script/jenkins/bench.sh')
+                  sh(label: 'Run benchmarks', script: './.ci/scripts/bench.sh')
                   sendBenchmarks(file: 'bench.out', index: "benchmark-server")
                 }
               }
@@ -366,7 +366,7 @@ pipeline {
               unstash 'source'
               dir("${BASE_DIR}"){
                 catchError(buildResult: 'SUCCESS', message: 'Sync Kibana is not updated', stageResult: 'UNSTABLE') {
-                  sh(label: 'Test Sync', script: './script/jenkins/sync.sh')
+                  sh(label: 'Test Sync', script: './.ci/scripts/sync.sh')
                 }
               }
             }
@@ -386,7 +386,7 @@ pipeline {
               golang(){
                 dockerLogin(secret: env.DOCKER_SECRET, registry: env.DOCKER_REGISTRY)
                 dir("${BASE_DIR}"){
-                  sh(label: 'Package & Push', script: "./script/jenkins/package-docker-snapshot.sh ${env.GIT_BASE_COMMIT} ${env.DOCKER_IMAGE}")
+                  sh(label: 'Package & Push', script: "./.ci/scripts/package-docker-snapshot.sh ${env.GIT_BASE_COMMIT} ${env.DOCKER_IMAGE}")
                 }
               }
               build(job: 'apm-server/apm-hey-test-benchmark', propagate: true, wait: true,
@@ -428,10 +428,10 @@ pipeline {
                   unstash 'source'
                   golang(){
                     dir("${BASE_DIR}"){
-                      sh(label: 'Build packages', script: './script/jenkins/package.sh')
-                      sh(label: 'Test packages install', script: './script/jenkins/test-install-packages.sh')
+                      sh(label: 'Build packages', script: './.ci/scripts/package.sh')
+                      sh(label: 'Test packages install', script: './.ci/scripts/test-install-packages.sh')
                       dockerLogin(secret: env.DOCKER_SECRET, registry: env.DOCKER_REGISTRY)
-                      sh(label: 'Package & Push', script: "./script/jenkins/package-docker-snapshot.sh ${env.GIT_BASE_COMMIT} ${env.DOCKER_IMAGE}")
+                      sh(label: 'Package & Push', script: "./.ci/scripts/package-docker-snapshot.sh ${env.GIT_BASE_COMMIT} ${env.DOCKER_IMAGE}")
                     }
                   }
                 }
diff --git a/script/jenkins/ci.ps1 b/script/jenkins/ci.ps1
deleted file mode 100755
index 770d7699d6d..00000000000
--- a/script/jenkins/ci.ps1
+++ /dev/null
@@ -1,67 +0,0 @@
-function Exec {
-    [CmdletBinding()]
-    param(
-        [Parameter(Mandatory = $true)]
-        [scriptblock]$cmd,
-        [string]$errorMessage = ($msgs.error_bad_command -f $cmd)
-    )
-
-    try {
-        $global:lastexitcode = 0
-        & $cmd
-        if ($lastexitcode -ne 0) {
-            throw $errorMessage
-        }
-    }
-    catch [Exception] {
-        throw $_
-    }
-}
-
-# Setup Go.
-$env:GOPATH = $env:WORKSPACE
-$env:PATH = "$env:GOPATH\bin;C:\tools\mingw64\bin;$env:PATH"
-& gvm --format=powershell $(Get-Content .go-version) | Invoke-Expression
-
-# Write cached magefile binaries to workspace to ensure
-# each run starts from a clean slate.
-$env:MAGEFILE_CACHE = "$env:WORKSPACE\.magefile"
-
-# Configure testing parameters.
-$env:TEST_COVERAGE = "true"
-$env:RACE_DETECTOR = "true"
-
-# Install mage from vendor.
-exec { go install github.com/elastic/apm-server/vendor/github.com/magefile/mage }
-
-echo "Fetching testing dependencies"
-# TODO (elastic/beats#5050): Use a vendored copy of this.
-exec { go get github.com/docker/libcompose }
-
-if (Test-Path "build") { Remove-Item -Recurse -Force build }
-New-Item -ItemType directory -Path build\coverage | Out-Null
-New-Item -ItemType directory -Path build\system-tests | Out-Null
-New-Item -ItemType directory -Path build\system-tests\run | Out-Null
-
-echo "Building fields.yml"
-exec { mage fields }
-
-echo "Building $env:beat"
-exec { mage build } "Build FAILURE"
-
-echo "Unit testing $env:beat"
-exec { mage goTestUnit }
-
-echo "System testing $env:beat"
-# Get a CSV list of package names.
-$packages = $(go list ./... | select-string -Pattern "/vendor/" -NotMatch | select-string -Pattern "/scripts/cmd/" -NotMatch)
-$packages = ($packages|group|Select -ExpandProperty Name) -join ","
-exec { go test -race -c -cover -covermode=atomic -coverpkg $packages } "go test FAILURE"
-
-echo "Running python tests"
-choco install python -y -r --no-progress --version 3.8.1.20200110
-refreshenv
-$env:PATH = "C:\Python38;C:\Python38\Scripts;$env:PATH"
-$env:PYTHON_ENV = "$env:TEMP\python-env"
-python --version
-exec { mage pythonUnitTest } "System test FAILURE"