diff --git a/src/poetry/console/commands/check.py b/src/poetry/console/commands/check.py
index ae90004d318..a79b7bc2be3 100644
--- a/src/poetry/console/commands/check.py
+++ b/src/poetry/console/commands/check.py
@@ -5,6 +5,7 @@
 from typing import ClassVar
 
 from cleo.helpers import option
+from poetry.core.utils.helpers import module_name
 
 from poetry.console.commands.command import Command
 
@@ -128,6 +129,46 @@ def _validate_dependencies_source(self, config: dict[str, Any]) -> list[str]:
             for source in sorted(all_referenced_sources - sources)
         ]
 
+    def _validate_project_in_src(
+        self, toml_data: dict[str, Any], base_path: Path | None
+    ) -> list[str]:
+        """
+        Checks the validity of projects located under src/ subdirectory.
+        """
+        result: list[str] = []
+
+        project_name = toml_data.get("project", {}).get("name") or toml_data.get(
+            "tool", {}
+        ).get("poetry", {}).get("name")
+
+        if project_name is None or base_path is None:
+            return result
+
+        project_name = module_name(project_name)
+
+        project_dir = base_path / project_name
+        src_project_dir = base_path / "src" / project_name
+
+        project_dir_empty = (
+            project_dir.exists()
+            and project_dir.is_dir()
+            and not any(project_dir.iterdir())
+        )
+        src_dir_not_empty = (
+            src_project_dir.exists()
+            and src_project_dir.is_dir()
+            and any(src_project_dir.iterdir())
+        )
+
+        if project_dir_empty and src_dir_not_empty:
+            result.append(
+                f"Found empty directory '{project_name}' in project root while the actual package is in "
+                f"'src/{project_name}'. This may cause issues with package installation. "
+                "Consider removing the empty directory."
+            )
+
+        return result
+
     def handle(self) -> int:
         from poetry.core.pyproject.toml import PyProjectTOML
 
@@ -149,6 +190,10 @@ def handle(self) -> int:
         check_result["errors"].extend(errors)
         check_result["warnings"].extend(warnings)
 
+        project_root = poetry_file.parent
+        warnings = self._validate_project_in_src(toml_data, project_root)
+        check_result["warnings"].extend(warnings)
+
         # Validate readme (files must exist)
         # TODO: consider [project.readme] as well
         if "readme" in poetry_config:
diff --git a/tests/console/commands/test_check.py b/tests/console/commands/test_check.py
index 6a23a2c093f..f40316d9e28 100644
--- a/tests/console/commands/test_check.py
+++ b/tests/console/commands/test_check.py
@@ -1,5 +1,7 @@
 from __future__ import annotations
 
+import os
+
 from typing import TYPE_CHECKING
 
 import pytest
@@ -59,6 +61,14 @@ def poetry_with_invalid_pyproject(
         yield Factory().create_poetry(cwd)
 
 
+@pytest.fixture
+def poetry_with_src_folder(
+    set_project_context: SetProjectContext,
+) -> Iterator[Poetry]:
+    with set_project_context("project_with_src_folder", in_place=False) as cwd:
+        yield Factory().create_poetry(cwd)
+
+
 @pytest.fixture()
 def tester(
     command_tester_factory: CommandTesterFactory, poetry_simple_project: Poetry
@@ -309,3 +319,24 @@ def test_check_does_not_error_on_pypi_reference(
 
     assert tester.io.fetch_output() == "All set!\n"
     assert status_code == 0
+
+
+def test_check_project_with_src_folder(
+    command_tester_factory: CommandTesterFactory,
+    poetry_with_src_folder: Poetry,
+) -> None:
+    tester = command_tester_factory("check", poetry=poetry_with_src_folder)
+
+    poetry_file = poetry_with_src_folder.file.path
+    project_root = poetry_file.parent
+    project_dir = project_root / "project_with_src_folder"
+    os.makedirs(project_dir, exist_ok=True)
+    tester.execute("")
+
+    expected = """\
+Warning: Found empty directory 'project_with_src_folder' in project root while the actual package is in\
+ 'src/project_with_src_folder'. This may cause issues with package installation.\
+ Consider removing the empty directory.
+"""
+
+    assert tester.io.fetch_error() == expected
diff --git a/tests/fixtures/project_with_src_folder/pyproject.toml b/tests/fixtures/project_with_src_folder/pyproject.toml
new file mode 100644
index 00000000000..e86df64968b
--- /dev/null
+++ b/tests/fixtures/project_with_src_folder/pyproject.toml
@@ -0,0 +1,12 @@
+[project]
+name = "project-with-src-folder"
+version = "1.2.3"
+description = "This is a description"
+authors = []
+license = "MIT"
+
+
+[tool.poetry]
+packages = []
+
+[tool.poetry.group.dev.dependencies]
diff --git a/tests/fixtures/project_with_src_folder/src/project_with_src_folder/__init__.py b/tests/fixtures/project_with_src_folder/src/project_with_src_folder/__init__.py
new file mode 100644
index 00000000000..e69de29bb2d