diff --git a/src/presets/cloudflare/utils.ts b/src/presets/cloudflare/utils.ts
index 47e8661e7b..397271b0da 100644
--- a/src/presets/cloudflare/utils.ts
+++ b/src/presets/cloudflare/utils.ts
@@ -322,16 +322,31 @@ export async function writeWranglerConfig(
   }
 
   // Read user config
-  const { config: userConfig = {} } = await readWranglerConfig(nitro);
+  const { configPath: userConfigPath, config: userConfig = {} } =
+    await readWranglerConfig(nitro);
 
   // Nitro context config (from frameworks and modules)
   const ctxConfig = nitro.options.cloudflare?.wrangler || {};
 
   // Validate and warn about overrides
   for (const key in overrides) {
-    if (key in userConfig || key in ctxConfig) {
+    let conflict: "ctx" | "user" | undefined;
+    if (key === "assets") {
+      conflict = findAssetsConflict(
+        overrides.assets!,
+        ctxConfig.assets,
+        userConfig.assets,
+        wranglerConfigDir,
+        userConfigPath ? dirname(userConfigPath) : nitro.options.rootDir
+      );
+    } else if (key in ctxConfig) {
+      conflict = "ctx";
+    } else if (key in userConfig) {
+      conflict = "user";
+    }
+    if (conflict) {
       nitro.logger.warn(
-        `[cloudflare] Wrangler config \`${key}\`${key in ctxConfig ? "set by config or modules" : ""} is overridden and will be ignored.`
+        `[cloudflare] Wrangler config \`${key}\`${conflict === "ctx" ? " set by config or modules" : ""} is overridden and will be ignored.`
       );
     }
   }
@@ -402,6 +417,36 @@ export async function writeWranglerConfig(
   );
 }
 
+type WranglerAssets = NonNullable<WranglerConfig["assets"]>;
+
+// Returns the source of an asset `binding` or `directory` that differs from the generated one
+// Context config is copied into the generated config (relative to `generatedDir`),
+// while user config paths are relative to the user wrangler config (`userDir`)
+function findAssetsConflict(
+  expected: WranglerAssets,
+  ctxAssets: Partial<WranglerAssets> | undefined,
+  userAssets: Partial<WranglerAssets> | undefined,
+  generatedDir: string,
+  userDir: string
+): "ctx" | "user" | undefined {
+  for (const field of ["binding", "directory"] as const) {
+    // Context config takes precedence over user config (null means unset in JSON)
+    const source = ctxAssets?.[field] == null ? "user" : "ctx";
+    const value = (source === "ctx" ? ctxAssets : userAssets)?.[field];
+    if (value == null) {
+      continue;
+    }
+    const isConflict =
+      field === "directory"
+        ? resolve(source === "ctx" ? generatedDir : userDir, value) !==
+          resolve(generatedDir, expected.directory!)
+        : value !== expected.binding;
+    if (isConflict) {
+      return source;
+    }
+  }
+}
+
 async function generateWorkerName(nitro: Nitro) {
   const gitConfig = await readGitConfig(nitro.options.rootDir).catch(
     () => undefined
diff --git a/test/unit/cloudflare-config.test.ts b/test/unit/cloudflare-config.test.ts
new file mode 100644
index 0000000000..c813df4dc7
--- /dev/null
+++ b/test/unit/cloudflare-config.test.ts
@@ -0,0 +1,129 @@
+import { mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { createNitro } from "nitropack/core";
+import { join, resolve } from "pathe";
+import { describe, expect, it, vi } from "vitest";
+
+describe("Cloudflare asset configuration diagnostics", () => {
+  it.each([
+    {
+      title: "routing policy",
+      fileAssets: { html_handling: "drop-trailing-slash" as const },
+      contextAssets: {},
+      warns: false,
+    },
+    {
+      title: "matching generated values",
+      fileAssets: { binding: "ASSETS", directory: "./.output/public" },
+      contextAssets: {},
+      warns: false,
+    },
+    {
+      title: "matching directory with trailing slash",
+      fileAssets: { directory: ".output/public/" },
+      contextAssets: {},
+      warns: false,
+    },
+    {
+      title: "matching directory with Windows separators",
+      fileAssets: { directory: ".\\.output\\public" },
+      contextAssets: {},
+      warns: false,
+    },
+    {
+      title: "unset asset fields from JSON",
+      fileAssets: { directory: null, binding: null },
+      contextAssets: {},
+      warns: false,
+    },
+    {
+      title: "conflicting file binding with context routing policy",
+      fileAssets: { binding: "CUSTOM" },
+      contextAssets: { html_handling: "drop-trailing-slash" as const },
+      warns: "file",
+    },
+    {
+      title: "context binding precedence",
+      fileAssets: { binding: "CUSTOM" },
+      contextAssets: { binding: "ASSETS" },
+      warns: false,
+    },
+    {
+      title: "conflicting context binding",
+      fileAssets: {},
+      contextAssets: { binding: "CUSTOM" },
+      warns: "context",
+    },
+    {
+      title: "conflicting asset directory",
+      fileAssets: { directory: "./custom" },
+      contextAssets: {},
+      warns: "file",
+    },
+    {
+      title: "file directory relative to generated config",
+      fileAssets: { directory: "../public" },
+      contextAssets: {},
+      warns: "file",
+    },
+    {
+      title: "matching context directory",
+      fileAssets: {},
+      contextAssets: { directory: "../public" },
+      warns: false,
+    },
+    {
+      title: "conflicting context directory",
+      fileAssets: {},
+      contextAssets: { directory: "./.output/public" },
+      warns: "context",
+    },
+  ])(
+    "reports $title correctly",
+    async ({ fileAssets, contextAssets, warns }) => {
+      const rootDir = await mkdtemp(
+        join(tmpdir(), "nitro-assets-diagnostics-")
+      );
+      await writeFile(
+        join(rootDir, "wrangler.json"),
+        JSON.stringify({ name: "test-worker", assets: fileAssets })
+      );
+      const nitro = await createNitro({
+        rootDir,
+        preset: "cloudflare-module",
+        compatibilityDate: "2026-09-30",
+        cloudflare: { deployConfig: true, wrangler: { assets: contextAssets } },
+      });
+      const warn = vi.spyOn(nitro.logger, "warn");
+      try {
+        await nitro.hooks.callHook("compiled", nitro);
+        const generated = JSON.parse(
+          await readFile(
+            join(nitro.options.output.serverDir, "wrangler.json"),
+            "utf8"
+          )
+        );
+        expect(generated.assets.binding).toBe("ASSETS");
+        expect(
+          resolve(nitro.options.output.serverDir, generated.assets.directory)
+        ).toBe(resolve(nitro.options.output.publicDir));
+        const message = warn.mock.calls
+          .map(([message]) => String(message))
+          .find((message) => message.includes("Wrangler config `assets`"));
+        expect(Boolean(message)).toBe(Boolean(warns));
+        if (message) {
+          expect(message.includes(" set by config or modules")).toBe(
+            warns === "context"
+          );
+        }
+        if ("html_handling" in contextAssets || "html_handling" in fileAssets) {
+          expect(generated.assets.html_handling).toBe("drop-trailing-slash");
+        }
+      } finally {
+        warn.mockRestore();
+        await nitro.close();
+        await rm(rootDir, { recursive: true, force: true });
+      }
+    }
+  );
+});