diff --git a/src/server/editorServices.ts b/src/server/editorServices.ts
index 23f8d844c9856..70d7db4f8781d 100644
--- a/src/server/editorServices.ts
+++ b/src/server/editorServices.ts
@@ -2935,8 +2935,10 @@ export class ProjectService {
             this.watchWildcards(configFilename, configFileExistenceInfo, project);
         }
         project.enablePluginsWithOptions(compilerOptions);
-        const filesToAdd = parsedCommandLine.fileNames.concat(project.getExternalFiles(ProgramUpdateLevel.Full));
-        this.updateRootAndOptionsOfNonInferredProject(project, filesToAdd, fileNamePropertyReader, compilerOptions, parsedCommandLine.typeAcquisition!, parsedCommandLine.compileOnSave, parsedCommandLine.watchOptions);
+        if (!project.hasPluginSetExtraFileExtensions) {
+            const filesToAdd = parsedCommandLine.fileNames.concat(project.getExternalFiles(ProgramUpdateLevel.Full));
+            this.updateRootAndOptionsOfNonInferredProject(project, filesToAdd, fileNamePropertyReader, compilerOptions, parsedCommandLine.typeAcquisition!, parsedCommandLine.compileOnSave, parsedCommandLine.watchOptions);
+        }
         tracing?.pop();
     }
 
diff --git a/src/server/project.ts b/src/server/project.ts
index 90205d695015c..879b849873c30 100644
--- a/src/server/project.ts
+++ b/src/server/project.ts
@@ -375,6 +375,14 @@ export abstract class Project implements LanguageServiceHost, ModuleResolutionHo
     /** @internal */
     protected readonly plugins: PluginModuleWithName[] = [];
 
+    /**
+     * Used to determine whether enabled plugins have modified extra file extensions through ProjectService.setHostConfiguration
+     * See: https://github.com/microsoft/TypeScript/issues/61302
+     *
+     * @internal
+     */
+    hasPluginSetExtraFileExtensions = false;
+
     /**
      * This is map from files to unresolved imports in it
      * Maop does not contain entries for files that do not have unresolved imports
@@ -2147,6 +2155,11 @@ export abstract class Project implements LanguageServiceHost, ModuleResolutionHo
                 return;
             }
 
+            if (this.plugins.some(p => p.name === configEntry.name)) {
+                this.hasPluginSetExtraFileExtensions = true;
+                return;
+            }
+
             const info: PluginCreateInfo = {
                 config: configEntry,
                 project: this,