diff --git a/conan/tools/gnu/autotoolstoolchain.py b/conan/tools/gnu/autotoolstoolchain.py
index e4c008553ce..e24105b37b7 100644
--- a/conan/tools/gnu/autotoolstoolchain.py
+++ b/conan/tools/gnu/autotoolstoolchain.py
@@ -86,8 +86,13 @@ def __init__(self, conanfile, namespace=None, prefix="/"):
                 self._build = _get_gnu_triplet(os_build, arch_build, compiler=compiler)["triplet"]
 
         sysroot = self._conanfile.conf.get("tools.build:sysroot")
-        sysroot = sysroot.replace("\\", "/") if sysroot is not None else None
-        self.sysroot_flag = "--sysroot {}".format(sysroot) if sysroot else None
+        if sysroot:
+            root = sysroot.replace("\\", "/")
+            compiler = self._conanfile.settings.get_safe("compiler")
+            self.sysroot_flag = f"--sysroot {root}" if compiler != "qcc" else f"-Wc,-isysroot,{root}"
+        else:
+            self.sysroot_flag = None
+
         extra_configure_args = self._conanfile.conf.get("tools.gnu:extra_configure_args",
                                                         check_type=list,
                                                         default=[])
diff --git a/conan/tools/gnu/gnutoolchain.py b/conan/tools/gnu/gnutoolchain.py
index 421be382a47..542ffacf5ff 100644
--- a/conan/tools/gnu/gnutoolchain.py
+++ b/conan/tools/gnu/gnutoolchain.py
@@ -91,8 +91,13 @@ def __init__(self, conanfile, namespace=None, prefix="/"):
                 self.triplets_info["build"] = _get_gnu_triplet(os_build, arch_build, compiler=compiler)
 
         sysroot = self._conanfile.conf.get("tools.build:sysroot")
-        sysroot = sysroot.replace("\\", "/") if sysroot is not None else None
-        self.sysroot_flag = "--sysroot {}".format(sysroot) if sysroot else None
+        if sysroot:
+            root = sysroot.replace("\\", "/")
+            compiler = self._conanfile.settings.get_safe("compiler")
+            self.sysroot_flag = f"--sysroot {root}" if compiler != "qcc" else f"-Wc,-isysroot,{root}"
+        else:
+            self.sysroot_flag = None
+
         self.configure_args = {}
         self.autoreconf_args = {"--force": None, "--install": None}
         self.make_args = {}
diff --git a/test/unittests/client/toolchain/__init__.py b/test/unittests/client/toolchain/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/test/unittests/client/toolchain/autotools/__init__.py b/test/unittests/client/toolchain/autotools/__init__.py
deleted file mode 100644
index e69de29bb2d..00000000000
diff --git a/test/unittests/client/tools/apple/test_xcodebuild.py b/test/unittests/tools/apple/test_xcodebuild.py
similarity index 100%
rename from test/unittests/client/tools/apple/test_xcodebuild.py
rename to test/unittests/tools/apple/test_xcodebuild.py
diff --git a/test/unittests/client/toolchain/autotools/autotools_test.py b/test/unittests/tools/gnu/autotools_test_old.py
similarity index 100%
rename from test/unittests/client/toolchain/autotools/autotools_test.py
rename to test/unittests/tools/gnu/autotools_test_old.py
diff --git a/test/unittests/client/toolchain/autotools/autotools_toolchain_test.py b/test/unittests/tools/gnu/autotools_toolchain_test.py
similarity index 97%
rename from test/unittests/client/toolchain/autotools/autotools_toolchain_test.py
rename to test/unittests/tools/gnu/autotools_toolchain_test.py
index 5e06e9ad0af..b6536e91588 100644
--- a/test/unittests/client/toolchain/autotools/autotools_toolchain_test.py
+++ b/test/unittests/tools/gnu/autotools_toolchain_test.py
@@ -485,6 +485,21 @@ def test_sysrootflag():
     assert expected in env["LDFLAGS"]
 
 
+def test_sysrootflag_qnx():
+    """Even when no cross building it is adjusted because it could target a Mac version"""
+    conanfile = ConanFileMock()
+    conanfile.conf.define("tools.build:sysroot", "/path/to/sysroot")
+    conanfile.settings = MockSettings(
+        {"compiler": "qcc",
+         "build_type": "Debug",
+         "os": "Linux",
+         "arch": "x86_64"})
+    conanfile.settings_build = conanfile.settings
+    be = AutotoolsToolchain(conanfile)
+    expected = "-Wc,-isysroot,/path/to/sysroot"
+    assert be.sysroot_flag == expected
+
+
 def test_custom_defines():
     conanfile = ConanFileMock()
     conanfile.conf.define("tools.apple:sdk_path", "/path/to/sdk")
diff --git a/test/unittests/tools/gnu/test_gnutoolchain.py b/test/unittests/tools/gnu/test_gnutoolchain.py
index badab8a7b7e..4b19e261fdd 100644
--- a/test/unittests/tools/gnu/test_gnutoolchain.py
+++ b/test/unittests/tools/gnu/test_gnutoolchain.py
@@ -166,6 +166,21 @@ def test_linker_scripts():
     assert "-T'path_to_second_linker_script'" in env["LDFLAGS"]
 
 
+def test_sysrootflag_qnx():
+    """Even when no cross building it is adjusted because it could target a Mac version"""
+    conanfile = ConanFileMock()
+    conanfile.conf.define("tools.build:sysroot", "/path/to/sysroot")
+    conanfile.settings = MockSettings(
+        {"compiler": "qcc",
+         "build_type": "Debug",
+         "os": "Linux",
+         "arch": "x86_64"})
+    conanfile.settings_build = conanfile.settings
+    be = GnuToolchain(conanfile)
+    expected = "-Wc,-isysroot,/path/to/sysroot"
+    assert be.sysroot_flag == expected
+
+
 def test_update_or_prune_any_args(cross_building_conanfile):
     # Issue: https://github.com/conan-io/conan/issues/12642
     at = GnuToolchain(cross_building_conanfile)