diff --git a/.chronus/changes/fix-list-files-across-instances-2026-0-9-17-57-50.md b/.chronus/changes/fix-list-files-across-instances-2026-0-9-17-57-50.md
new file mode 100644
index 00000000000..5a6c705d35f
--- /dev/null
+++ b/.chronus/changes/fix-list-files-across-instances-2026-0-9-17-57-50.md
@@ -0,0 +1,8 @@
+---
+# Change versionKind to one of: internal, fix, dependencies, feature, deprecation, breaking
+changeKind: fix
+packages:
+  - "@typespec/compiler"
+---
+
+Fix `--list-files` not working when multiple instance of compiler are loaded
diff --git a/packages/compiler/src/core/emitter-utils.ts b/packages/compiler/src/core/emitter-utils.ts
index 41e26d3a774..3f9fbfd5882 100644
--- a/packages/compiler/src/core/emitter-utils.ts
+++ b/packages/compiler/src/core/emitter-utils.ts
@@ -8,10 +8,19 @@ export interface EmitFileOptions {
   newLine?: NewLine;
 }
 
-const emittedFilesPaths: string[] = [];
-export function flushEmittedFilesPaths(): string[] {
-  return emittedFilesPaths.splice(0, emittedFilesPaths.length);
+const emittedFilesPerProgramKey = Symbol.for("TYPESPEC_EMITTED_FILES_PATHS");
+if ((globalThis as any)[emittedFilesPerProgramKey] === undefined) {
+  (globalThis as any)[emittedFilesPerProgramKey] = new WeakMap<Program, string[]>();
 }
+
+export function getEmittedFilesForProgram(program: Program): string[] {
+  const existing = (globalThis as any)[emittedFilesPerProgramKey].get(program);
+  if (existing) return existing;
+  const val: string[] = [];
+  (globalThis as any)[emittedFilesPerProgramKey].set(program, val);
+  return val;
+}
+
 /**
  * Helper to emit a file.
  * @param program TypeSpec Program
@@ -25,8 +34,7 @@ export async function emitFile(program: Program, options: EmitFileOptions): Prom
     options.newLine && options.newLine === "crlf"
       ? options.content.replace(/(\r\n|\n|\r)/gm, "\r\n")
       : options.content;
-
-  emittedFilesPaths.push(options.path);
+  getEmittedFilesForProgram(program).push(options.path);
 
   return await program.host.writeFile(options.path, content);
 }
diff --git a/packages/compiler/src/core/program.ts b/packages/compiler/src/core/program.ts
index d5038ab0343..b9548c358f6 100644
--- a/packages/compiler/src/core/program.ts
+++ b/packages/compiler/src/core/program.ts
@@ -16,7 +16,7 @@ import { createBinder } from "./binder.js";
 import { Checker, createChecker } from "./checker.js";
 import { createSuppressCodeFix } from "./compiler-code-fixes/suppress.codefix.js";
 import { compilerAssert } from "./diagnostics.js";
-import { flushEmittedFilesPaths } from "./emitter-utils.js";
+import { getEmittedFilesForProgram } from "./emitter-utils.js";
 import { resolveTypeSpecEntrypoint } from "./entrypoint-resolution.js";
 import { ExternalError } from "./external-error.js";
 import { getLibraryUrlsLoaded } from "./library.js";
@@ -196,7 +196,7 @@ export async function compile(
     const { duration } = await emit(emitter, program);
     emitStats.emitters[emitter.metadata.name ?? "<unnamed>"] = duration;
     if (options.listFiles) {
-      logEmittedFilesPath(host.logSink);
+      logEmittedFilesPath(program);
     }
   }
   emitStats.total = timer.end();
@@ -1014,10 +1014,10 @@ async function runEmitter(emitter: EmitterRef, program: Program) {
   }
 }
 
-function logEmittedFilesPath(logSink: LogSink) {
-  flushEmittedFilesPaths().forEach((filePath) => {
+function logEmittedFilesPath(program: Program) {
+  getEmittedFilesForProgram(program).forEach((filePath) => {
     // eslint-disable-next-line no-console
-    console.log(`    ${pc.dim(transformPathForSink(logSink, filePath))}`);
+    console.log(`    ${pc.dim(transformPathForSink(program.host.logSink, filePath))}`);
   });
 }
 function transformPathForSink(logSink: LogSink, path: string) {