diff --git a/.changeset/nice-sheep-juggle.md b/.changeset/nice-sheep-juggle.md
new file mode 100644
index 000000000..262615098
--- /dev/null
+++ b/.changeset/nice-sheep-juggle.md
@@ -0,0 +1,5 @@
+---
+"openapi-typescript": patch
+---
+
+Mirror directory structure of input files if output is a directory to prevent overwriting the same file again and again.
diff --git a/.gitignore b/.gitignore
index 28dd70cdf..c81238d0d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,5 @@
 .astro
 dist
 node_modules
+
+packages/openapi-typescript/test/fixtures/cli-outputs/out
diff --git a/packages/openapi-typescript/bin/cli.js b/packages/openapi-typescript/bin/cli.js
index c73b445c3..0e568e46e 100755
--- a/packages/openapi-typescript/bin/cli.js
+++ b/packages/openapi-typescript/bin/cli.js
@@ -114,13 +114,13 @@ async function generateSchema(pathToSpec) {
     let outputFilePath = new URL(flags.output, CWD); // note: may be directory
     const isDir = fs.existsSync(outputFilePath) && fs.lstatSync(outputFilePath).isDirectory();
     if (isDir) {
-      if (typeof flags.output === 'string' && !flags.output.endsWith('/')) {
-        outputFilePath = new URL(`${flags.output}/`, CWD)
+      if (typeof flags.output === "string" && !flags.output.endsWith("/")) {
+        outputFilePath = new URL(`${flags.output}/`, CWD);
       }
-      const filename = path.basename(pathToSpec).replace(EXT_RE, ".ts");
+      const filename = pathToSpec.replace(EXT_RE, ".ts");
       const originalOutputFilePath = outputFilePath;
       outputFilePath = new URL(filename, originalOutputFilePath);
-      if (outputFilePath.protocol !== 'file:') {
+      if (outputFilePath.protocol !== "file:") {
         outputFilePath = new URL(outputFilePath.host.replace(EXT_RE, ".ts"), originalOutputFilePath);
       }
     }
@@ -174,6 +174,8 @@ async function main() {
   // handle local schema(s)
   const inputSpecPaths = await glob(pathToSpec);
   const isGlob = inputSpecPaths.length > 1;
+  const isDirUrl = outputDir.pathname === outputFile.pathname;
+  const isFile = fs.existsSync(outputDir) && fs.lstatSync(outputDir).isFile();
 
   // error: no matches for glob
   if (inputSpecPaths.length === 0) {
@@ -182,7 +184,7 @@ async function main() {
   }
 
   // error: tried to glob output to single file
-  if (isGlob && output === OUTPUT_FILE && fs.existsSync(outputDir) && fs.lstatSync(outputDir).isFile()) {
+  if (isGlob && output === OUTPUT_FILE && (isFile || !isDirUrl)) {
     error(`Expected directory for --output if using glob patterns. Received "${flags.output}".`);
     process.exit(1);
   }
@@ -191,15 +193,14 @@ async function main() {
   await Promise.all(
     inputSpecPaths.map(async (specPath) => {
       if (flags.output !== "." && output === OUTPUT_FILE) {
-        if (isGlob) {
-          fs.mkdirSync(outputFile, { recursive: true }); // recursively make parent dirs
-        }
-        else {
+        if (isGlob || isDirUrl) {
+          fs.mkdirSync(new URL(path.dirname(specPath), outputDir), { recursive: true }); // recursively make parent dirs
+        } else {
           fs.mkdirSync(outputDir, { recursive: true }); // recursively make parent dirs
         }
       }
       await generateSchema(specPath);
-    })
+    }),
   );
 }
 
diff --git a/packages/openapi-typescript/test/cli.test.ts b/packages/openapi-typescript/test/cli.test.ts
index 8acf3537c..88ae34d3d 100644
--- a/packages/openapi-typescript/test/cli.test.ts
+++ b/packages/openapi-typescript/test/cli.test.ts
@@ -1,13 +1,22 @@
 import { execa } from "execa";
+import glob from "fast-glob";
 import fs from "node:fs";
+import path from "node:path/posix"; // prevent issues with `\` on windows
 import { URL, fileURLToPath } from "node:url";
 import os from "node:os";
 
 const root = new URL("../", import.meta.url);
 const cwd = os.platform() === "win32" ? fileURLToPath(root) : root; // execa bug: fileURLToPath required on Windows
 const cmd = "./bin/cli.js";
+const inputDir = "test/fixtures/cli-outputs/";
+const outputDir = path.join(inputDir, "out/");
 const TIMEOUT = 90000;
 
+// fast-glob does not sort results
+async function getOutputFiles() {
+  return (await glob("**", { cwd: outputDir })).sort((a, b) => a.localeCompare(b, undefined, { numeric: true }));
+}
+
 describe("CLI", () => {
   // note: the snapshots in index.test.ts test the Node API; these test the CLI
   describe("snapshots", () => {
@@ -76,4 +85,59 @@ describe("CLI", () => {
       expect(stdout).toEqual(expect.stringMatching(/^v[\d.]+(-.*)?$/));
     });
   });
+
+  describe("outputs", () => {
+    beforeEach(() => {
+      fs.rmSync(new URL(outputDir, root), { recursive: true, force: true });
+    });
+
+    test("single file to file", async () => {
+      const inputFile = path.join(inputDir, "file-a.yaml");
+      const outputFile = path.join(outputDir, "file-a.ts");
+      await execa(cmd, [inputFile, "--output", outputFile], { cwd });
+      const result = await getOutputFiles();
+      expect(result).toEqual(["file-a.ts"]);
+    });
+
+    test("single file to directory", async () => {
+      const inputFile = path.join(inputDir, "file-a.yaml");
+      await execa(cmd, [inputFile, "--output", outputDir], { cwd });
+      const result = await getOutputFiles();
+      expect(result).toEqual(["test/fixtures/cli-outputs/file-a.ts"]);
+    });
+
+    test("single file (glob) to file", async () => {
+      const inputFile = path.join(inputDir, "*-a.yaml");
+      const outputFile = path.join(outputDir, "file-a.ts");
+      await execa(cmd, [inputFile, "--output", outputFile], { cwd });
+      const result = await getOutputFiles();
+      expect(result).toEqual(["file-a.ts"]);
+    });
+
+    test("multiple files to file", async () => {
+      const inputFile = path.join(inputDir, "*.yaml");
+      const outputFile = path.join(outputDir, "file-a.ts");
+      await expect(execa(cmd, [inputFile, "--output", outputFile], { cwd })).rejects.toThrow();
+    });
+
+    test("multiple files to directory", async () => {
+      const inputFile = path.join(inputDir, "*.yaml");
+      await execa(cmd, [inputFile, "--output", outputDir], { cwd });
+      const result = await getOutputFiles();
+      expect(result).toEqual(["test/fixtures/cli-outputs/file-a.ts", "test/fixtures/cli-outputs/file-b.ts"]);
+    });
+
+    test("multiple nested files to directory", async () => {
+      const inputFile = path.join(inputDir, "**/*.yaml");
+      await execa(cmd, [inputFile, "--output", outputDir], { cwd });
+      const result = await getOutputFiles();
+      expect(result).toEqual([
+        "test/fixtures/cli-outputs/file-a.ts",
+        "test/fixtures/cli-outputs/file-b.ts",
+        "test/fixtures/cli-outputs/nested/deep/file-e.ts",
+        "test/fixtures/cli-outputs/nested/file-c.ts",
+        "test/fixtures/cli-outputs/nested/file-d.ts",
+      ]);
+    });
+  });
 });
diff --git a/packages/openapi-typescript/test/fixtures/cli-outputs/file-a.yaml b/packages/openapi-typescript/test/fixtures/cli-outputs/file-a.yaml
new file mode 100644
index 000000000..7f4eaac81
--- /dev/null
+++ b/packages/openapi-typescript/test/fixtures/cli-outputs/file-a.yaml
@@ -0,0 +1,8 @@
+openapi: "3.0"
+info:
+  title: test file a
+  version: "1.0"
+paths:
+  /endpoint:
+    get:
+      description: OK
diff --git a/packages/openapi-typescript/test/fixtures/cli-outputs/file-b.yaml b/packages/openapi-typescript/test/fixtures/cli-outputs/file-b.yaml
new file mode 100644
index 000000000..e41219cf3
--- /dev/null
+++ b/packages/openapi-typescript/test/fixtures/cli-outputs/file-b.yaml
@@ -0,0 +1,8 @@
+openapi: "3.0"
+info:
+  title: test file b
+  version: "1.0"
+paths:
+  /endpoint:
+    get:
+      description: OK
diff --git a/packages/openapi-typescript/test/fixtures/cli-outputs/nested/deep/file-e.yaml b/packages/openapi-typescript/test/fixtures/cli-outputs/nested/deep/file-e.yaml
new file mode 100644
index 000000000..fc56849d8
--- /dev/null
+++ b/packages/openapi-typescript/test/fixtures/cli-outputs/nested/deep/file-e.yaml
@@ -0,0 +1,8 @@
+openapi: "3.0"
+info:
+  title: test file e
+  version: "1.0"
+paths:
+  /endpoint:
+    get:
+      description: OK
diff --git a/packages/openapi-typescript/test/fixtures/cli-outputs/nested/file-c.yaml b/packages/openapi-typescript/test/fixtures/cli-outputs/nested/file-c.yaml
new file mode 100644
index 000000000..ccf725a95
--- /dev/null
+++ b/packages/openapi-typescript/test/fixtures/cli-outputs/nested/file-c.yaml
@@ -0,0 +1,8 @@
+openapi: "3.0"
+info:
+  title: test file c
+  version: "1.0"
+paths:
+  /endpoint:
+    get:
+      description: OK
diff --git a/packages/openapi-typescript/test/fixtures/cli-outputs/nested/file-d.yaml b/packages/openapi-typescript/test/fixtures/cli-outputs/nested/file-d.yaml
new file mode 100644
index 000000000..27079dd0c
--- /dev/null
+++ b/packages/openapi-typescript/test/fixtures/cli-outputs/nested/file-d.yaml
@@ -0,0 +1,8 @@
+openapi: "3.0"
+info:
+  title: test file d
+  version: "1.0"
+paths:
+  /endpoint:
+    get:
+      description: OK