diff --git a/src/core/knitr.ts b/src/core/knitr.ts
index d525c97ea28..beb69903efd 100644
--- a/src/core/knitr.ts
+++ b/src/core/knitr.ts
@@ -11,6 +11,8 @@ import { rBinaryPath, resourcePath } from "./resources.ts";
 import { readYamlFromString } from "./yaml.ts";
 import { coerce, satisfies } from "semver/mod.ts";
 import { debug } from "../deno_ral/log.ts";
+import { isWindows } from "../deno_ral/platform.ts";
+import { isWindowsArm } from "./windows.ts";
 
 export interface KnitrCapabilities {
   versionMajor: number;
@@ -18,6 +20,7 @@ export interface KnitrCapabilities {
   versionPatch: number;
   home: string;
   libPaths: string[];
+  platform?: string;
   packages: KnitrRequiredPackages;
 }
 
@@ -68,6 +71,28 @@ export async function checkRBinary() {
   }
 }
 
+export class WindowsArmX64RError extends Error {
+  constructor(msg: string) {
+    super(msg);
+  }
+}
+
+function checkWindowsArmR(platform: string | undefined): void {
+  if (!platform) return;
+
+  const isX64R = platform.includes("x86_64") || platform.includes("i386");
+
+  if (isX64R && isWindowsArm()) {
+    throw new WindowsArmX64RError(
+      "x64 R detected on Windows ARM.\n\n" +
+        "x64 R runs under emulation and is not reliable for Quarto.\n" +
+        "Please install native ARM64 R. \n" +
+        "Read about R on 64-bit Windows ARM at https://blog.r-project.org/2024/04/23/r-on-64-bit-arm-windows/\n" +
+        "After installation, set QUARTO_R environment variable if the correct version is not correctly found.",
+    );
+  }
+}
+
 export async function knitrCapabilities(rBin: string | undefined) {
   if (!rBin) return undefined;
   try {
@@ -105,6 +130,7 @@ export async function knitrCapabilities(rBin: string | undefined) {
           Object.values(pkgVersRequirement["rmarkdown"]).join(" "),
         )
         : false;
+
       return caps;
     } else {
       debug("\n++ Problem with results of knitr capabilities check.");
@@ -115,9 +141,35 @@ export async function knitrCapabilities(rBin: string | undefined) {
       if (result.stderr) {
         debug(`    with stderr from R:\n${result.stderr}`);
       }
+
+      // Check if this is x64 R on Windows ARM
+      if (result.stdout) {
+        try {
+          const yamlMatch = result.stdout.match(
+            /--- YAML_START ---(.*)--- YAML_END ---/s,
+          );
+          if (yamlMatch) {
+            const yamlLines = yamlMatch[1];
+            const caps = readYamlFromString(yamlLines) as KnitrCapabilities;
+            checkWindowsArmR(caps.platform);
+          }
+        } catch (e) {
+          // If it's our specific x64-on-ARM error, rethrow it
+          if (e instanceof WindowsArmX64RError) {
+            throw e;
+          }
+          // Otherwise YAML parse failed, continue to return undefined
+          debug("    Failed to parse YAML for architecture detection");
+        }
+      }
+
       return undefined;
     }
-  } catch {
+  } catch (e) {
+    // Rethrow x64-on-ARM errors - these have helpful messages
+    if (e instanceof WindowsArmX64RError) {
+      throw e;
+    }
     debug(
       `\n++ Error while running 'capabilities/knitr.R' ${
         rBin ? "with " + rBin : ""
@@ -136,6 +188,12 @@ export function knitrCapabilitiesMessage(caps: KnitrCapabilities, indent = "") {
   for (const path of caps.libPaths) {
     lines.push(`  - ${path}`);
   }
+
+  // Show platform information if available
+  if (caps.platform) {
+    lines.push(`Platform: ${caps.platform}`);
+  }
+
   lines.push(`knitr: ${caps.packages.knitr || "(None)"}`);
   if (caps.packages.knitr && !caps.packages.knitrVersOk) {
     lines.push(
diff --git a/src/core/windows.ts b/src/core/windows.ts
index aed3d21fab8..1c0b09e63ea 100644
--- a/src/core/windows.ts
+++ b/src/core/windows.ts
@@ -163,3 +163,64 @@ export async function safeWindowsExec(
     removeIfExists(tempFile);
   }
 }
+
+// Detect Windows ARM hardware using IsWow64Process2 API
+// Returns true if running on ARM64 hardware (even from x64 Deno under emulation)
+//
+// Background: Deno.build.arch reports the architecture Deno was compiled for,
+// not the actual hardware architecture. When x64 Deno runs on ARM64 under
+// WOW64 emulation, Deno.build.arch still reports "x86_64".
+//
+// Solution: Use Windows IsWow64Process2 API which returns the native machine
+// architecture regardless of emulation. This is a standard Windows API function
+// available since Windows 10 (kernel32.dll is always present on Windows).
+//
+// Reference: Validated approach from https://github.com/cderv/quarto-windows-arm
+// See: https://learn.microsoft.com/en-us/windows/win32/api/wow64apiset/nf-wow64apiset-iswow64process2
+export function isWindowsArm(): boolean {
+  if (!isWindows) {
+    return false;
+  }
+
+  try {
+    // Load kernel32.dll
+    const kernel32 = Deno.dlopen("kernel32.dll", {
+      IsWow64Process2: {
+        parameters: ["pointer", "pointer", "pointer"],
+        result: "i32",
+      },
+      GetCurrentProcess: {
+        parameters: [],
+        result: "pointer",
+      },
+    });
+
+    // Get current process handle
+    const hProcess = kernel32.symbols.GetCurrentProcess();
+
+    // Prepare output parameters - allocate buffer for USHORT (2 bytes each)
+    const processMachineBuffer = new Uint16Array(1);
+    const nativeMachineBuffer = new Uint16Array(1);
+
+    // Call IsWow64Process2 with pointers to buffers
+    const result = kernel32.symbols.IsWow64Process2(
+      hProcess,
+      Deno.UnsafePointer.of(processMachineBuffer),
+      Deno.UnsafePointer.of(nativeMachineBuffer),
+    );
+
+    kernel32.close();
+
+    if (result === 0) {
+      // Function failed
+      return false;
+    }
+
+    // IMAGE_FILE_MACHINE_ARM64 = 0xAA64 = 43620
+    const IMAGE_FILE_MACHINE_ARM64 = 0xAA64;
+    return nativeMachineBuffer[0] === IMAGE_FILE_MACHINE_ARM64;
+  } catch {
+    // IsWow64Process2 not available (Windows < 10) or other error
+    return false;
+  }
+}
diff --git a/src/execute/rmd.ts b/src/execute/rmd.ts
index 3cbfd02e2be..4b78c0605a9 100644
--- a/src/execute/rmd.ts
+++ b/src/execute/rmd.ts
@@ -26,6 +26,7 @@ import {
   knitrCapabilitiesMessage,
   knitrInstallationMessage,
   rInstallationMessage,
+  WindowsArmX64RError,
 } from "../core/knitr.ts";
 import {
   DependenciesOptions,
@@ -139,13 +140,23 @@ title: "Title"
     const kMessage = "Checking R installation...........";
     let caps: KnitrCapabilities | undefined;
     let rBin: string | undefined;
+    let x64ArmError: WindowsArmX64RError | undefined;
     const json: Record<string, unknown> = {};
     if (conf.jsonResult) {
       (conf.jsonResult.tools as Record<string, unknown>).knitr = json;
     }
     const knitrCb = async () => {
       rBin = await checkRBinary();
-      caps = await knitrCapabilities(rBin);
+      try {
+        caps = await knitrCapabilities(rBin);
+      } catch (e) {
+        if (e instanceof WindowsArmX64RError) {
+          x64ArmError = e;
+          // Don't rethrow - let caps stay undefined but capture error
+        } else {
+          throw e; // Rethrow other errors
+        }
+      }
     };
     if (conf.jsonResult) {
       await knitrCb();
@@ -205,6 +216,16 @@ title: "Title"
       checkInfoMsg(msg);
       json["installed"] = false;
       checkInfoMsg("");
+    } else if (x64ArmError) {
+      // x64 R on Windows ARM detected - show specific error
+      json["installed"] = false;
+      checkCompleteMessage(kMessage + "(None)\n");
+      const errorLines = x64ArmError.message.split("\n");
+      errorLines.forEach((line) => {
+        checkInfoMsg(line);
+      });
+      json["error"] = x64ArmError.message;
+      checkInfoMsg("");
     } else if (caps === undefined) {
       json["installed"] = false;
       checkCompleteMessage(kMessage + "(None)\n");
diff --git a/src/resources/capabilities/knitr.R b/src/resources/capabilities/knitr.R
index 3d82a8a910d..17b0a6fbf78 100644
--- a/src/resources/capabilities/knitr.R
+++ b/src/resources/capabilities/knitr.R
@@ -8,6 +8,7 @@ cat("libPaths:\n")
 for (lib in .libPaths()) {
   cat(paste0('  - ', shQuote(lib)), "\n")
 }
+cat("platform:", R.version[['platform']], "\n")
 cat("packages:\n")
 cat("  knitr: ")
 if (requireNamespace("knitr", quietly = TRUE)) {