diff --git a/CHANGELOG.md b/CHANGELOG.md
index f2733013a..bae5b5d0a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -43,7 +43,8 @@ mounting and running matplotblib on some machines. Re-instantiated a disabled te
 
 ### Removed
 
-- ([#520](https://github.com/microsoft/InnerEye-DeepLearning/pull/520)) Disable glaucoma job from Azure pipeline.
+-  ([#542](https://github.com/microsoft/InnerEye-DeepLearning/pull/542)) Removed Windows test leg from build pipeline.
+-  ([#520](https://github.com/microsoft/InnerEye-DeepLearning/pull/520)) Disable glaucoma job from Azure pipeline.
 
 ### Deprecated
 
diff --git a/azure-pipelines/build-pr.yml b/azure-pipelines/build-pr.yml
index 58b61c6c5..750f77c46 100644
--- a/azure-pipelines/build-pr.yml
+++ b/azure-pipelines/build-pr.yml
@@ -21,7 +21,7 @@ jobs:
     pool:
       vmImage: 'windows-2019'
     steps:
-      - template: build.yaml
+      - template: build_windows.yaml
 
   - job: Linux
     pool:
diff --git a/azure-pipelines/build.yaml b/azure-pipelines/build.yaml
index 1a5d8dfeb..a03b3f5a7 100644
--- a/azure-pipelines/build.yaml
+++ b/azure-pipelines/build.yaml
@@ -1,19 +1,6 @@
 steps:
   - template: checkout.yml
 
-  - task: CredScan@3
-    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
-
-  - task: PostAnalysis@1
-    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
-    displayName: 'Post Analysis'
-    inputs:
-      CredScan: true
-
-  - script: echo %NUMBER_OF_PROCESSORS%
-    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
-    displayName: Print processors
-
   - bash: |
       conda env create --file environment.yml --name InnerEye --quiet
       source activate InnerEye
diff --git a/azure-pipelines/build_windows.yaml b/azure-pipelines/build_windows.yaml
new file mode 100644
index 000000000..25b67bac6
--- /dev/null
+++ b/azure-pipelines/build_windows.yaml
@@ -0,0 +1,20 @@
+steps:
+  - template: checkout_windows.yml
+
+  - task: CredScan@3
+    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
+
+  - task: PostAnalysis@1
+    condition: and(succeeded(), eq( variables['Agent.OS'], 'Windows_NT' ))
+    displayName: 'Post Analysis'
+    inputs:
+      CredScan: true
+
+  - task: ComponentGovernanceComponentDetection@0
+    condition: succeeded()
+    inputs:
+      scanType: 'Register'
+      verbosity: 'Normal'
+      alertWarningLevel: 'High'
+      failOnAlert: true
+      failOnStderr: true
diff --git a/azure-pipelines/checkout.yml b/azure-pipelines/checkout.yml
index 88665f705..05efcfd5f 100644
--- a/azure-pipelines/checkout.yml
+++ b/azure-pipelines/checkout.yml
@@ -4,10 +4,7 @@ steps:
     submodules: true
 
   - bash: |
-      if [ $(Agent.OS) = 'Windows_NT' ]
-      then subdir=Scripts
-      else subdir=bin
-      fi
+      subdir=bin
       echo "Adding this directory to PATH: $CONDA/$subdir"
       echo "##vso[task.prependpath]$CONDA/$subdir"
     displayName: Add conda to PATH
@@ -19,7 +16,6 @@ steps:
       conda list
     displayName: Print conda version and initial package list
 
-  # Linux only; not needed for Windows
   - bash: |
       sudo chown -R $USER /usr/share/miniconda
     condition: and(succeeded(), eq( variables['Agent.OS'], 'Linux' ))
diff --git a/azure-pipelines/checkout_windows.yml b/azure-pipelines/checkout_windows.yml
new file mode 100644
index 000000000..44a0a26b9
--- /dev/null
+++ b/azure-pipelines/checkout_windows.yml
@@ -0,0 +1,17 @@
+steps:
+  - checkout: self
+    lfs: true
+    submodules: true
+
+  - bash: |
+      subdir=Scripts
+      echo "Adding this directory to PATH: $CONDA/$subdir"
+      echo "##vso[task.prependpath]$CONDA/$subdir"
+    displayName: Add conda to PATH
+    condition: succeeded()
+
+  - bash: |
+      conda install conda=4.8.3 -y
+      conda --version
+      conda list
+    displayName: Print conda version and initial package list