diff --git a/src/reboot_manager.py b/src/reboot_manager.py
index 9ca6fc4..3259fae 100644
--- a/src/reboot_manager.py
+++ b/src/reboot_manager.py
@@ -231,8 +231,9 @@ exit
         if callback:
             callback("progress", "Running JTAG system reset...")
 
+        from vitis_checker import build_tool_command
         result = subprocess.run(
-            [xsct, tcl_path],
+            build_tool_command(xsct, tcl_path),
             capture_output=True,
             text=True,
             timeout=30,
diff --git a/src/vitis_checker.py b/src/vitis_checker.py
index 877036b..683a969 100644
--- a/src/vitis_checker.py
+++ b/src/vitis_checker.py
@@ -110,6 +110,7 @@ def _scan_xilinx_root(
     """Scan xilinx_root for all installed versions of a tool.
 
     Searches under Vitis/*/bin/ and Vivado/*/bin/ for the executable.
+    On Windows also checks .bat wrappers in addition to .exe.
 
     Args:
         xilinx_root: Xilinx root directory (e.g., /data/xilinx, C:/Xilinx).
@@ -124,6 +125,11 @@ def _scan_xilinx_root(
     if not xr.is_dir():
         return results
 
+    # On Windows, also try .bat extension (Xilinx tools use .bat wrappers)
+    suffixes = [exec_suffix]
+    if exec_suffix == ".exe":
+        suffixes.append(".bat")
+
     for product in _PRODUCT_DIRS:
         pdir = xr / product
         if not pdir.is_dir():
@@ -135,11 +141,13 @@ def _scan_xilinx_root(
         for ver_dir in entries:
             if not ver_dir.is_dir():
                 continue
-            candidate = ver_dir / "bin" / f"{exec_name}{exec_suffix}"
-            if candidate.is_file():
-                v = _parse_version_tuple(ver_dir.name)
-                if v != (0,):
-                    results.append((v, candidate, product))
+            for sfx in suffixes:
+                candidate = ver_dir / "bin" / f"{exec_name}{sfx}"
+                if candidate.is_file():
+                    v = _parse_version_tuple(ver_dir.name)
+                    if v != (0,):
+                        results.append((v, candidate, product))
+                    break  # Found for this version dir
     # Sort newest first (descending version tuple)
     results.sort(key=lambda x: x[0], reverse=True)
     return results
@@ -237,6 +245,60 @@ def get_all_found_versions(
     ]
 
 
+# ── Environment setup ────────────────────────────────────────────────
+
+
+def _find_settings_script(tool_path: str) -> str | None:
+    """Find the settings64 script for a Xilinx tool's version directory.
+
+    Walks up from the tool's bin/ directory looking for
+    settings64.sh (Linux) or settings64.bat (Windows).
+
+    Args:
+        tool_path: Absolute path to a Xilinx tool executable.
+
+    Returns:
+        Path to settings64 script, or None if not found.
+    """
+    p = Path(tool_path).resolve()
+    for parent in p.parents:
+        for name in ("settings64.sh", "settings64.bat"):
+            candidate = parent / name
+            if candidate.is_file():
+                return str(candidate)
+    return None
+
+
+def build_tool_command(tool_path: str, *args: str) -> list[str]:
+    """Build a subprocess-safe command with Xilinx environment setup.
+
+    On Linux: sources settings64.sh before running the tool.
+    On Windows: .bat wrappers handle environment internally.
+
+    Args:
+        tool_path: Path to the Xilinx tool executable.
+        *args: Arguments to pass to the tool.
+
+    Returns:
+        Command list suitable for subprocess.run().
+    """
+    import shlex
+
+    system = platform.system().lower()
+
+    # Windows: .bat wrappers set up their own environment
+    if system == "windows":
+        return [tool_path, *args]
+
+    # Linux: find settings64.sh and source it before running
+    settings = _find_settings_script(tool_path)
+    if not settings:
+        return [tool_path, *args]
+
+    quoted = " ".join(shlex.quote(a) for a in [tool_path, *args])
+    return ["bash", "-c", f"source {shlex.quote(settings)} && {quoted}"]
+
+
 # ── Public path getters ──────────────────────────────────────────────