diff --git a/csharp/tools/pre-finalize.cmd b/csharp/tools/pre-finalize.cmd
index 0ee982b6585..b20e2bf77d8 100644
--- a/csharp/tools/pre-finalize.cmd
+++ b/csharp/tools/pre-finalize.cmd
@@ -5,6 +5,7 @@ type NUL && "%CODEQL_DIST%\codeql" database index-files ^
     --include-extension=.csproj ^
     --include-extension=.props ^
     --include-extension=.xml ^
+    --also-match-lgtm-index-filters ^
     --size-limit 10m ^
     --language xml ^
     --working-dir=. ^
diff --git a/csharp/tools/pre-finalize.sh b/csharp/tools/pre-finalize.sh
index b0abd28f9ee..409fb252da3 100755
--- a/csharp/tools/pre-finalize.sh
+++ b/csharp/tools/pre-finalize.sh
@@ -7,6 +7,7 @@ set -eu
     --include-extension=.csproj \
     --include-extension=.props \
     --include-extension=.xml \
+    --also-match-lgtm-index-filters \
     --size-limit 10m \
     --language xml \
     --working-dir=. \
diff --git a/go/codeql-tools/pre-finalize.cmd b/go/codeql-tools/pre-finalize.cmd
index 4abac249933..66f6e80a69f 100644
--- a/go/codeql-tools/pre-finalize.cmd
+++ b/go/codeql-tools/pre-finalize.cmd
@@ -9,6 +9,7 @@ if NOT "%CODEQL_EXTRACTOR_GO_EXTRACT_HTML%"=="no" (
                         --include-extension=.xhtm ^
                         --include-extension=.xhtml ^
                         --include-extension=.vue ^
+                        --also-match-lgtm-index-filters ^
                         --size-limit 10m ^
                         --language html ^
                         -- ^
diff --git a/go/codeql-tools/pre-finalize.sh b/go/codeql-tools/pre-finalize.sh
index 3a8b31c70a0..9cf0b7ae0b1 100755
--- a/go/codeql-tools/pre-finalize.sh
+++ b/go/codeql-tools/pre-finalize.sh
@@ -10,6 +10,7 @@ if [ "${CODEQL_EXTRACTOR_GO_EXTRACT_HTML:-yes}" != "no" ]; then
                         --include-extension=.xhtm \
                         --include-extension=.xhtml \
                         --include-extension=.vue \
+                        --also-match-lgtm-index-filters \
                         --size-limit 10m \
                         --language html \
                         -- \
diff --git a/python/tools/pre-finalize.cmd b/python/tools/pre-finalize.cmd
index 07454671062..235b79c77b0 100644
--- a/python/tools/pre-finalize.cmd
+++ b/python/tools/pre-finalize.cmd
@@ -3,6 +3,7 @@
 type NUL && "%CODEQL_DIST%\codeql" database index-files ^
     --include-extension=.yaml ^
     --include-extension=.yml ^
+    --also-match-lgtm-index-filters ^
     --size-limit=5m ^
     --language yaml ^
     -- ^
diff --git a/python/tools/pre-finalize.sh b/python/tools/pre-finalize.sh
index 9fe5200a38f..b938be75aa7 100755
--- a/python/tools/pre-finalize.sh
+++ b/python/tools/pre-finalize.sh
@@ -5,6 +5,7 @@ set -eu
 "$CODEQL_DIST/codeql" database index-files \
     --include-extension=.yaml \
     --include-extension=.yml \
+    --also-match-lgtm-index-filters \
     --size-limit=5m \
     --language yaml \
     -- \
diff --git a/ql/tools/pre-finalize.cmd b/ql/tools/pre-finalize.cmd
index 49d18f3d197..19fa7b04523 100644
--- a/ql/tools/pre-finalize.cmd
+++ b/ql/tools/pre-finalize.cmd
@@ -3,6 +3,7 @@
 type NUL && "%CODEQL_DIST%\codeql" database index-files ^
     --include=**/qlpack.yml ^
     --include-extension=.qlref ^
+    --also-match-lgtm-index-filters ^
     --size-limit=5m ^
     --language yaml ^
     -- ^
diff --git a/ql/tools/pre-finalize.sh b/ql/tools/pre-finalize.sh
index 7003ad81c1b..afae94ef83a 100755
--- a/ql/tools/pre-finalize.sh
+++ b/ql/tools/pre-finalize.sh
@@ -5,6 +5,7 @@ set -eu
 "$CODEQL_DIST/codeql" database index-files \
     "--include=**/qlpack.yml" \
     --include-extension=.qlref \
+    --also-match-lgtm-index-filters \
     --size-limit=5m \
     --language yaml \
     -- \