diff --git a/.github/workflows/build_desktop_and_deploy.yaml b/.github/workflows/build_desktop_and_deploy.yaml
index a2b3dfec71..0455b7e37c 100644
--- a/.github/workflows/build_desktop_and_deploy.yaml
+++ b/.github/workflows/build_desktop_and_deploy.yaml
@@ -78,7 +78,7 @@ jobs:
         strategy:
             matrix:
                 arch: [x64, arm64]
-        uses: ./.github/workflows/build_windows.yaml
+        uses: ./.github/workflows/build_desktop_windows.yaml
         secrets: inherit # zizmor: ignore[secrets-inherit]
         with:
             sign: true
@@ -89,7 +89,7 @@ jobs:
         if: github.event_name != 'workflow_dispatch' || inputs.macos
         needs: prepare
         name: macOS
-        uses: ./.github/workflows/build_macos.yaml
+        uses: ./.github/workflows/build_desktop_macos.yaml
         secrets: inherit # zizmor: ignore[secrets-inherit]
         with:
             sign: true
@@ -104,7 +104,7 @@ jobs:
             matrix:
                 arch: [amd64, arm64]
                 sqlcipher: [static]
-        uses: ./.github/workflows/build_linux.yaml
+        uses: ./.github/workflows/build_desktop_linux.yaml
         with:
             arch: ${{ matrix.arch }}
             sqlcipher: ${{ matrix.sqlcipher }}
diff --git a/.github/workflows/build_desktop_and_test.yaml b/.github/workflows/build_desktop_and_test.yaml
index fa62d2642a..6996a42465 100644
--- a/.github/workflows/build_desktop_and_test.yaml
+++ b/.github/workflows/build_desktop_and_test.yaml
@@ -20,7 +20,7 @@ jobs:
     windows:
         needs: fetch
         name: Windows
-        uses: ./.github/workflows/build_windows.yaml
+        uses: ./.github/workflows/build_desktop_windows.yaml
         strategy:
             matrix:
                 arch: [x64, ia32, arm64]
@@ -31,7 +31,7 @@ jobs:
     linux:
         needs: fetch
         name: "Linux (${{ matrix.arch }}) (sqlcipher: ${{ matrix.sqlcipher }})"
-        uses: ./.github/workflows/build_linux.yaml
+        uses: ./.github/workflows/build_desktop_linux.yaml
         strategy:
             matrix:
                 sqlcipher: [system, static]
@@ -44,7 +44,7 @@ jobs:
     macos:
         needs: fetch
         name: macOS
-        uses: ./.github/workflows/build_macos.yaml
+        uses: ./.github/workflows/build_desktop_macos.yaml
         with:
             blob_report: true
 
@@ -70,10 +70,11 @@ jobs:
               uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8
               with:
                   pattern: blob-report-*
-                  path: all-blob-reports
+                  path: apps/desktop/all-blob-reports
                   merge-multiple: true
 
             - name: Merge into HTML Report
+              working-directory: apps/desktop
               run: pnpm playwright merge-reports -c ./playwright.config.ts --reporter=html ./all-blob-reports
 
             - name: Upload HTML report
@@ -81,7 +82,7 @@ jobs:
               uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7
               with:
                   name: html-report
-                  path: playwright-report
+                  path: apps/desktop/playwright-report
                   retention-days: 14
 
             - if: contains(needs.*.result, 'failure') || contains(needs.*.result, 'cancelled')
diff --git a/.github/workflows/build_desktop_linux.yaml b/.github/workflows/build_desktop_linux.yaml
index 4f2964ba53..456036e277 100644
--- a/.github/workflows/build_desktop_linux.yaml
+++ b/.github/workflows/build_desktop_linux.yaml
@@ -164,7 +164,7 @@ jobs:
                     -e SQLCIPHER_BUNDLED \
                     -e CI=1 \
                     $HAK_DOCKER_IMAGE \
-                    pnpm build:native
+                    pnpm run build:native
 
             - name: Fix permissions
               working-directory: apps/desktop
@@ -192,7 +192,7 @@ jobs:
 
             - name: Build App
               working-directory: apps/desktop
-              run: pnpm build --publish never $BUILD_ARGS -l $TARGETS
+              run: pnpm run build --publish never $BUILD_ARGS -l $TARGETS
               env:
                   VARIANT_PATH: variant.json
                   # Only set for Nightly builds
diff --git a/.github/workflows/build_desktop_macos.yaml b/.github/workflows/build_desktop_macos.yaml
index 38f3ac51e9..e763a1018c 100644
--- a/.github/workflows/build_desktop_macos.yaml
+++ b/.github/workflows/build_desktop_macos.yaml
@@ -128,14 +128,14 @@ jobs:
             - name: Build Natives
               if: steps.cache.outputs.cache-hit != 'true'
               working-directory: apps/desktop
-              run: pnpm build:native:universal
+              run: pnpm run build:native:universal
 
             # We split these because electron-builder gets upset if we set CSC_LINK even to an empty string
             - name: "[Signed] Build App"
               if: inputs.sign != ''
               working-directory: apps/desktop
               run: |
-                  pnpm build:universal --publish never -m ${TARGETS}
+                  pnpm run build:universal --publish never -m ${TARGETS}
               env:
                   APPLE_TEAM_ID: ${{ secrets.APPLE_TEAM_ID }}
                   APPLE_ID: ${{ secrets.APPLE_ID }}
@@ -160,7 +160,7 @@ jobs:
               if: inputs.sign == ''
               working-directory: apps/desktop
               run: |
-                  pnpm build:universal --publish never -m ${TARGETS}
+                  pnpm run build:universal --publish never -m ${TARGETS}
               env:
                   CSC_IDENTITY_AUTO_DISCOVERY: false
                   VARIANT_PATH: variant.json
diff --git a/.github/workflows/build_desktop_prepare.yaml b/.github/workflows/build_desktop_prepare.yaml
index b984717ee0..9889d7ec5c 100644
--- a/.github/workflows/build_desktop_prepare.yaml
+++ b/.github/workflows/build_desktop_prepare.yaml
@@ -79,7 +79,7 @@ jobs:
                   pnpm --cwd element-web install --frozen-lockfile
                   pnpm --cwd element-web run build
                   mv element-web/webapp .
-                  pnpm asar-webapp
+                  pnpm run asar-webapp
               env:
                   # These must be set for branch-match.sh to get the right branch
                   REPOSITORY: ${{ github.repository }}
diff --git a/.github/workflows/build_desktop_windows.yaml b/.github/workflows/build_desktop_windows.yaml
index 737cb822b9..3c07ea4947 100644
--- a/.github/workflows/build_desktop_windows.yaml
+++ b/.github/workflows/build_desktop_windows.yaml
@@ -194,7 +194,7 @@ jobs:
               working-directory: apps/desktop
               run: |
                   refreshenv
-                  pnpm build:native --target $env:TARGET
+                  pnpm run build:native --target $env:TARGET
               env:
                   TARGET: ${{ steps.config.outputs.target }}
 
@@ -244,7 +244,7 @@ jobs:
 
             - name: Build App
               working-directory: apps/desktop
-              run: pnpm build --publish never $BUILD_ARGS -w $TARGETS
+              run: pnpm run build --publish never $BUILD_ARGS -w $TARGETS
               shell: bash
               env:
                   VARIANT_PATH: variant.json
diff --git a/.github/workflows/dockerbuild.yaml b/.github/workflows/dockerbuild.yaml
index 31a4cc2c61..ad9868adb1 100644
--- a/.github/workflows/dockerbuild.yaml
+++ b/.github/workflows/dockerbuild.yaml
@@ -34,7 +34,7 @@ jobs:
             - name: Build test image
               uses: docker/build-push-action@d08e5c354a6adb9ed34480a06d141179aa583294 # v7
               with:
-                  file: dockerbuild/Dockerfile
+                  file: apps/desktop/dockerbuild/Dockerfile
                   push: false
                   load: true
                   tags: element-desktop-dockerbuild
@@ -65,7 +65,7 @@ jobs:
               if: github.event_name != 'pull_request'
               uses: docker/build-push-action@d08e5c354a6adb9ed34480a06d141179aa583294 # v7
               with:
-                  file: dockerbuild/Dockerfile
+                  file: apps/desktop/dockerbuild/Dockerfile
                   push: true
                   tags: ${{ steps.meta.outputs.tags }}
                   labels: ${{ steps.meta.outputs.labels }}