diff --git a/CHANGELOG.md b/CHANGELOG.md
index 80d63d0395..8c88a0243d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -32,6 +32,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - `opentelemetry-instrumentation-httpx` Fix `RequestInfo`/`ResponseInfo` type hints
   ([#3105](https://github.com/open-telemetry/opentelemetry-python-contrib/pull/3105))
+- `opentelemetry-instrumentation-click` Disable tracing of well-known server click commands
+  ([#3174](https://github.com/open-telemetry/opentelemetry-python-contrib/pull/3174))
 - `opentelemetry-instrumentation` Fix `get_dist_dependency_conflicts` if no distribution requires
   ([#3168](https://github.com/open-telemetry/opentelemetry-python-contrib/pull/3168))
 
diff --git a/instrumentation/opentelemetry-instrumentation-click/src/opentelemetry/instrumentation/click/__init__.py b/instrumentation/opentelemetry-instrumentation-click/src/opentelemetry/instrumentation/click/__init__.py
index 8222bfdf5a..e820ca7d87 100644
--- a/instrumentation/opentelemetry-instrumentation-click/src/opentelemetry/instrumentation/click/__init__.py
+++ b/instrumentation/opentelemetry-instrumentation-click/src/opentelemetry/instrumentation/click/__init__.py
@@ -13,7 +13,9 @@
 # limitations under the License.
 
 """
-Instrument `click`_ CLI applications.
+Instrument `click`_ CLI applications. The instrumentor will avoid instrumenting
+well-known servers (e.g. *flask run* and *uvicorn*) to avoid unexpected effects
+like every request having the same Trace ID.
 
 .. _click: https://pypi.org/project/click/
 
@@ -47,6 +49,12 @@ def hello():
 import click
 from wrapt import wrap_function_wrapper
 
+try:
+    from flask.cli import ScriptInfo as FlaskScriptInfo
+except ImportError:
+    FlaskScriptInfo = None
+
+
 from opentelemetry import trace
 from opentelemetry.instrumentation.click.package import _instruments
 from opentelemetry.instrumentation.click.version import __version__
@@ -66,6 +74,20 @@ def hello():
 _logger = getLogger(__name__)
 
 
+def _skip_servers(ctx: click.Context):
+    # flask run
+    if (
+        ctx.info_name == "run"
+        and FlaskScriptInfo
+        and isinstance(ctx.obj, FlaskScriptInfo)
+    ):
+        return True
+    # uvicorn
+    if ctx.info_name == "uvicorn":
+        return True
+    return False
+
+
 def _command_invoke_wrapper(wrapped, instance, args, kwargs, tracer):
     # Subclasses of Command include groups and CLI runners, but
     # we only want to instrument the actual commands which are
@@ -74,6 +96,12 @@ def _command_invoke_wrapper(wrapped, instance, args, kwargs, tracer):
         return wrapped(*args, **kwargs)
 
     ctx = args[0]
+
+    # we don't want to create a root span for long running processes like servers
+    # otherwise all requests would have the same trace id
+    if _skip_servers(ctx):
+        return wrapped(*args, **kwargs)
+
     span_name = ctx.info_name
     span_attributes = {
         PROCESS_COMMAND_ARGS: sys.argv,
diff --git a/instrumentation/opentelemetry-instrumentation-click/test-requirements.txt b/instrumentation/opentelemetry-instrumentation-click/test-requirements.txt
index 6e9162ccde..e07bd05bb7 100644
--- a/instrumentation/opentelemetry-instrumentation-click/test-requirements.txt
+++ b/instrumentation/opentelemetry-instrumentation-click/test-requirements.txt
@@ -1,7 +1,12 @@
 asgiref==3.8.1
+blinker==1.7.0
 click==8.1.7
 Deprecated==1.2.14
+Flask==3.0.2
 iniconfig==2.0.0
+itsdangerous==2.1.2
+Jinja2==3.1.4
+MarkupSafe==2.1.2
 packaging==24.0
 pluggy==1.5.0
 py-cpuinfo==9.0.0
@@ -9,7 +14,11 @@ pytest==7.4.4
 pytest-asyncio==0.23.5
 tomli==2.0.1
 typing_extensions==4.12.2
+Werkzeug==3.0.6
 wrapt==1.16.0
 zipp==3.19.2
 -e opentelemetry-instrumentation
 -e instrumentation/opentelemetry-instrumentation-click
+-e instrumentation/opentelemetry-instrumentation-flask
+-e instrumentation/opentelemetry-instrumentation-wsgi
+-e util/opentelemetry-util-http
diff --git a/instrumentation/opentelemetry-instrumentation-click/tests/test_click.py b/instrumentation/opentelemetry-instrumentation-click/tests/test_click.py
index 41d01a5bb4..1b07f6ab56 100644
--- a/instrumentation/opentelemetry-instrumentation-click/tests/test_click.py
+++ b/instrumentation/opentelemetry-instrumentation-click/tests/test_click.py
@@ -16,8 +16,14 @@
 from unittest import mock
 
 import click
+import pytest
 from click.testing import CliRunner
 
+try:
+    from flask import cli as flask_cli
+except ImportError:
+    flask_cli = None
+
 from opentelemetry.instrumentation.click import ClickInstrumentor
 from opentelemetry.test.test_base import TestBase
 from opentelemetry.trace import SpanKind
@@ -60,7 +66,7 @@ def command():
         )
 
     @mock.patch("sys.argv", ["flask", "command"])
-    def test_flask_run_command_wrapping(self):
+    def test_flask_command_wrapping(self):
         @click.command()
         def command():
             pass
@@ -162,6 +168,27 @@ def command_raises():
             },
         )
 
+    def test_uvicorn_cli_command_ignored(self):
+        @click.command("uvicorn")
+        def command_uvicorn():
+            pass
+
+        runner = CliRunner()
+        result = runner.invoke(command_uvicorn)
+        self.assertEqual(result.exit_code, 0)
+
+        self.assertFalse(self.memory_exporter.get_finished_spans())
+
+    @pytest.mark.skipif(flask_cli is None, reason="requires flask")
+    def test_flask_run_command_ignored(self):
+        runner = CliRunner()
+        result = runner.invoke(
+            flask_cli.run_command, obj=flask_cli.ScriptInfo()
+        )
+        self.assertEqual(result.exit_code, 2)
+
+        self.assertFalse(self.memory_exporter.get_finished_spans())
+
     def test_uninstrument(self):
         ClickInstrumentor().uninstrument()