diff --git a/packages/repo-tools/src/commands/api-reports/api-extractor.ts b/packages/repo-tools/src/commands/api-reports/api-extractor.ts
index 4546b292c8..70b4e54739 100644
--- a/packages/repo-tools/src/commands/api-reports/api-extractor.ts
+++ b/packages/repo-tools/src/commands/api-reports/api-extractor.ts
@@ -407,7 +407,6 @@ export async function runApiExtraction({
         packageEntryPoint.name === 'index' ? '' : `-${packageEntryPoint.name}`;
       const reportFileName = `report${suffix}`;
       const reportPath = resolvePath(projectFolder, reportFileName);
-      remainingReportFiles.delete(reportFileName);
 
       const warningCountBefore = await countApiReportWarnings(reportPath);
 
@@ -485,6 +484,11 @@ export async function runApiExtraction({
         ignoreMissingEntryPoint: true,
       });
 
+      // remove extracted reports from current list
+      for (const reportConfig of extractorConfig.reportConfigs) {
+        remainingReportFiles.delete(reportConfig.fileName);
+      }
+
       // The `packageFolder` needs to point to the location within `dist-types` in order for relative
       // paths to be logged. Unfortunately the `prepare` method above derives it from the `packageJsonFullPath`,
       // which needs to point to the actual file, so we override `packageFolder` afterwards.