diff --git a/packages/core/src/templates/create-project-from-template.test.ts b/packages/core/src/templates/create-project-from-template.test.ts
index fe9d3166..e31b0be2 100644
--- a/packages/core/src/templates/create-project-from-template.test.ts
+++ b/packages/core/src/templates/create-project-from-template.test.ts
@@ -160,6 +160,49 @@ describe("createProjectFromTemplate", () => {
     expect(artifacts.networks.testnet.dependencyGraph).toEqual({});
   });
 
+  // #90: in merge mode, placeholder substitution must touch only the files the
+  // template copied — never a user's pre-existing files.
+  it("should_not_replace_placeholders_in_pre_existing_files_in_merge_mode", async () => {
+    tmpDir = await mkdtemp(path.join(os.tmpdir(), "caatinga-merge-"));
+    const templateDir = path.join(tmpDir, "template");
+    const targetDir = path.join(tmpDir, "existing-app");
+    await mkdir(templateDir);
+    await writeFile(
+      path.join(templateDir, "caatinga.template.json"),
+      JSON.stringify({
+        name: "merge-template",
+        version: "0.1.0",
+        caatinga: { compatibleCore: "^3.0.0", templateVersion: 1 },
+        frontend: { framework: "vite-react", packageManager: "npm" },
+        contracts: { path: "contracts", default: "counter" },
+        files: { config: "caatinga.config.ts", artifacts: "caatinga.artifacts.json" },
+      }),
+      "utf8"
+    );
+    await writeFile(
+      path.join(templateDir, "caatinga.config.ts"),
+      'export default { project: "__PROJECT_NAME__" };\n',
+      "utf8"
+    );
+
+    // A pre-existing user file that is NOT part of the template but happens to
+    // contain the placeholder token.
+    await mkdir(targetDir, { recursive: true });
+    await writeFile(path.join(targetDir, "README.md"), "# __PROJECT_NAME__ notes\n", "utf8");
+
+    await createProjectFromTemplate({
+      projectName: "my-dapp",
+      targetDir,
+      templateDir,
+      filter: (relativePath) => relativePath === "caatinga.config.ts",
+    });
+
+    // The copied template file had its placeholder replaced …
+    expect(await readFile(path.join(targetDir, "caatinga.config.ts"), "utf8")).toContain("my-dapp");
+    // … while the user's pre-existing file was left byte-for-byte untouched.
+    expect(await readFile(path.join(targetDir, "README.md"), "utf8")).toBe("# __PROJECT_NAME__ notes\n");
+  });
+
   it("should_fail_when_template_manifest_is_missing", async () => {
     tmpDir = await mkdtemp(path.join(os.tmpdir(), "caatinga-init-"));
     const templateDir = path.join(tmpDir, "template");
diff --git a/packages/core/src/templates/create-project-from-template.ts b/packages/core/src/templates/create-project-from-template.ts
index 9143254c..c261e989 100644
--- a/packages/core/src/templates/create-project-from-template.ts
+++ b/packages/core/src/templates/create-project-from-template.ts
@@ -38,15 +38,27 @@ export async function createProjectFromTemplate(options: CreateProjectFromTempla
   const manifest = await readTemplateManifest(templateDir);
 
   const mergeIntoExisting = Boolean(options.filter);
+  // #90: in merge mode, record exactly which relative paths the copy writes so
+  // variable substitution never touches a user's pre-existing files.
+  const copiedRelPaths = mergeIntoExisting ? new Set<string>() : undefined;
   await mkdir(targetDir, { recursive: true });
   await cp(templateDir, targetDir, {
     recursive: true,
     force: true,
     errorOnExist: false,
-    filter: (source) => shouldCopyTemplateEntry(templateDir, source, options.filter),
+    filter: (source) => {
+      const keep = shouldCopyTemplateEntry(templateDir, source, options.filter);
+      if (keep && copiedRelPaths) {
+        const rel = path.relative(templateDir, source);
+        if (rel) {
+          copiedRelPaths.add(rel);
+        }
+      }
+      return keep;
+    },
   });
 
-  await replaceTemplateVariables(targetDir, options.projectName);
+  await replaceTemplateVariables(targetDir, options.projectName, copiedRelPaths);
   if (!mergeIntoExisting) {
     await ensureArtifacts(targetDir, options.projectName);
   }
@@ -113,7 +125,12 @@ async function readTemplateManifest(templateDir: string): Promise<TemplateManife
   }
 }
 
-async function replaceTemplateVariables(dir: string, projectName: string): Promise<void> {
+async function replaceTemplateVariables(
+  dir: string,
+  projectName: string,
+  allowlist?: ReadonlySet<string>,
+  rootDir: string = dir
+): Promise<void> {
   const entries = await readdir(dir);
 
   await Promise.all(
@@ -136,7 +153,7 @@ async function replaceTemplateVariables(dir: string, projectName: string): Promi
       }
 
       if (entryStat.isDirectory()) {
-        await replaceTemplateVariables(entryPath, projectName);
+        await replaceTemplateVariables(entryPath, projectName, allowlist, rootDir);
         return;
       }
 
@@ -144,6 +161,12 @@ async function replaceTemplateVariables(dir: string, projectName: string): Promi
         return;
       }
 
+      // #90: in merge mode, only substitute in files the template actually
+      // copied — never in a user's pre-existing files.
+      if (allowlist && !allowlist.has(path.relative(rootDir, entryPath))) {
+        return;
+      }
+
       const content = await readFile(entryPath, "utf8");
       await writeFile(entryPath, content.replaceAll("__PROJECT_NAME__", projectName), "utf8");
     })