diff --git a/src/CodeCoverage.php b/src/CodeCoverage.php
index 9c8853025..d96f5ab2a 100644
--- a/src/CodeCoverage.php
+++ b/src/CodeCoverage.php
@@ -414,15 +414,15 @@ private function applyCoversAndUsesFilter(RawCodeCoverageData $rawData, array|fa
 
     private function applyFilter(RawCodeCoverageData $data): void
     {
-        if ($this->filter->isEmpty()) {
-            return;
-        }
-
-        foreach (array_keys($data->lineCoverage()) as $filename) {
-            if ($this->filter->isExcluded($filename)) {
-                $data->removeCoverageDataForFile($filename);
+        if (!$this->filter->isEmpty()) {
+            foreach (array_keys($data->lineCoverage()) as $filename) {
+                if ($this->filter->isExcluded($filename)) {
+                    $data->removeCoverageDataForFile($filename);
+                }
             }
         }
+
+        $data->skipEmptyLines();
     }
 
     private function applyExecutableLinesFilter(RawCodeCoverageData $data): void
diff --git a/src/Data/RawCodeCoverageData.php b/src/Data/RawCodeCoverageData.php
index 444f410a7..9b4304648 100644
--- a/src/Data/RawCodeCoverageData.php
+++ b/src/Data/RawCodeCoverageData.php
@@ -103,8 +103,6 @@ private function __construct(array $lineCoverage, array $functionCoverage)
     {
         $this->lineCoverage     = $lineCoverage;
         $this->functionCoverage = $functionCoverage;
-
-        $this->skipEmptyLines();
     }
 
     public function clear(): void
@@ -251,7 +249,7 @@ public function removeCoverageDataForLines(string $filename, array $lines): void
      *
      * @see https://github.com/sebastianbergmann/php-code-coverage/issues/799
      */
-    private function skipEmptyLines(): void
+    public function skipEmptyLines(): void
     {
         foreach ($this->lineCoverage as $filename => $coverage) {
             foreach ($this->getEmptyLinesForFile($filename) as $emptyLine) {
diff --git a/tests/tests/Data/RawCodeCoverageDataTest.php b/tests/tests/Data/RawCodeCoverageDataTest.php
index 98c4f45cb..0d2470dd5 100644
--- a/tests/tests/Data/RawCodeCoverageDataTest.php
+++ b/tests/tests/Data/RawCodeCoverageDataTest.php
@@ -326,6 +326,7 @@ public function testCoverageForFileWithInlineAnnotations(): void
                 33,
             ],
         );
+        $coverage->skipEmptyLines();
 
         $this->assertEquals(
             [