diff --git a/.yamato/upm-ci.yml b/.yamato/upm-ci.yml
index ad36998e5f..c4d550e511 100644
--- a/.yamato/upm-ci.yml
+++ b/.yamato/upm-ci.yml
@@ -12,7 +12,7 @@
     flavor: {{ platform.flavor }}
   variables:
     EDITOR_VERSION: {{ editor.version }}
-  commands:
+  commands:        
     - {{ utr_install_win }}
     - {{ upm_ci_install }}
     # Get version 2.3.0-preview of doctools package (it currently fails for 3.0.0-preview).
@@ -26,7 +26,7 @@
     - upm-ci package pack --package-path ./Packages/com.unity.inputsystem/
     # Run upm-ci verification tests as well as tests contained in the package.
     - upm-ci package test --package-path ./Packages/com.unity.inputsystem/ -u %EDITOR_VERSION%
-      {% if platform.name == "win" %} --enable-code-coverage --code-coverage-options "generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem" 
+      {% if platform.name == "win" %} --enable-code-coverage --code-coverage-options "generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem;pathReplacePatterns:@*,,Library/PackageCache,Packages" 
       --extra-utr-arg="--coverage-results-path={{ yamato_source_dir_win }}/upm-ci~/test-results/CodeCoverage/Package" {% endif %}
     {% if platform.installscript %}
     - {{ unity_downloader_install }}
@@ -38,6 +38,13 @@
     - move /Y .\Packages\com.unity.inputsystem\Samples.meta .\Assets
     # Now run our full test suite that sits in Assets/Tests by running UTR on our project.
     - ./utr --testproject . --timeout=1200 --editor-location=.Editor --artifacts_path=upm-ci~/test-results/isolation-com.unity.inputsystem.tests --suite=playmode {% if platform.name == "win" %} --suite=editor {% endif %} {% if category.name == "performance" %} --category=Performance {% endif %} --api-profile=NET_4_6 {% if platform.runtime %} --platform {{ platform.runtime }} {% endif %} {% if platform.scripting-backend %} --scripting-backend {{ platform.scripting-backend }} {% endif %} --report-performance-data --performance-project-id=InputSystem {% if platform.name == "win" %}--enable-code-coverage --coverage-options="generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem" --coverage-results-path={{ yamato_source_dir_win }}/upm-ci~/test-results/CodeCoverage/Project {% endif %}
+    # Merge all the code coverage results into one report.
+    {% if platform.name == "win" %}
+    - '{{ yamato_source_dir_win }}/.Editor/Unity.exe -projectPath {{ yamato_source_dir_win }} -batchmode -debugCodeOptimization -enableCodeCoverage -coverageResultsPath {{ yamato_source_dir_win }}/upm-ci~/test-results/CodeCoverage/ -coverageOptions "generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem;sourcePaths:{{ yamato_source_dir_win }}/Packages/com.unity.inputsystem/" -quit' 
+    #delete the reports from the two runs and only keep the final merged one
+    - rmdir /s/q "{{ yamato_source_dir_win }}/upm-ci~/test-results/CodeCoverage/Package"
+    - rmdir /s/q "{{ yamato_source_dir_win }}/upm-ci~/test-results/CodeCoverage/Project"   
+    {% endif %}
   after:
     - {{ instabilities_install_win }}
     - {{ instabilities_run_win }}  
@@ -70,7 +77,7 @@
     - mv ./Assets/Samples.meta ./Packages/com.unity.inputsystem
     - upm-ci package pack --package-path ./Packages/com.unity.inputsystem/
     # Run upm-ci verification tests as well as tests contained in the package.
-    - upm-ci package test --package-path ./Packages/com.unity.inputsystem/ -u $EDITOR_VERSION {% if platform.name == "mac" or platform.name == "linux" %} --enable-code-coverage --code-coverage-options "generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem" --extra-utr-arg="--coverage-results-path={{ yamato_source_dir_nix }}/upm-ci~/test-results/CodeCoverage/Package" {% endif %}
+    - upm-ci package test --package-path ./Packages/com.unity.inputsystem/ -u $EDITOR_VERSION {% if platform.name == "mac" or platform.name == "linux" %} --enable-code-coverage --code-coverage-options "generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem;pathReplacePatterns:@*,,Library/PackageCache,Packages" --extra-utr-arg="--coverage-results-path={{ yamato_source_dir_nix }}/upm-ci~/test-results/CodeCoverage/Package" {% endif %}
     {% if platform.installscript %}
     - {{ unity_downloader_install }}
     - {{ platform.installscript }} $EDITOR_VERSION
@@ -81,6 +88,15 @@
     - mv ./Packages/com.unity.inputsystem/Samples.meta ./Assets
     # Now run our full test suite that sits in Assets/Tests by running UTR on our project.
     - ./utr --testproject . --timeout=1200 --editor-location=.Editor --artifacts_path=upm-ci~/test-results/isolation-com.unity.inputsystem.tests --suite=playmode {% if platform.name == "mac" or platform.name == "linux"%} --suite=editor {% endif %} {% if category.name == "performance" %} --category=Performance {% endif %} --api-profile=NET_4_6 {% if platform.runtime %} --platform {{ platform.runtime }} {% endif %} {% if platform.scripting-backend %} --scripting-backend {{ platform.scripting-backend }} {% endif %} --report-performance-data --performance-project-id=InputSystem {% if platform.name == "mac" or platform.name == "linux" %} --enable-code-coverage --coverage-options="generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem" --coverage-results-path={{ yamato_source_dir_nix }}/upm-ci~/test-results/CodeCoverage/Project {% endif %}
+    # Merge all the code coverage results into one report.
+    {% if platform.name == "mac" %}
+    - '{{ yamato_source_dir_nix }}/.Editor/Unity.app/Contents/MacOS/Unity -projectPath {{ yamato_source_dir_nix }} -batchmode -debugCodeOptimization -enableCodeCoverage -coverageResultsPath {{ yamato_source_dir_nix }}/upm-ci~/test-results/CodeCoverage/ -coverageOptions "generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem;sourcePaths:{{ yamato_source_dir_nix }}/Packages/com.unity.inputsystem/" -quit' 
+    {% endif %}
+    {% if platform.name == "linux" %}
+    - '{{ yamato_source_dir_nix }}/.Editor/Unity -projectPath {{ yamato_source_dir_nix }} -batchmode -debugCodeOptimization -enableCodeCoverage -coverageResultsPath {{ yamato_source_dir_nix }}/upm-ci~/test-results/CodeCoverage/ -coverageOptions "generateAdditionalMetrics;generateHtmlReport;assemblyFilters:+Unity.InputSystem;sourcePaths:{{ yamato_source_dir_nix }}/Packages/com.unity.inputsystem/" -quit' 
+    {% endif %}
+    - rm -rf {{ yamato_source_dir_nix }}/upm-ci~/test-results/CodeCoverage/Package
+    - rm -rf {{ yamato_source_dir_nix }}/upm-ci~/test-results/CodeCoverage/Project  
   after:
     - {{ instabilities_install_nix }}
     - {{ platform.instabilities_run }}