diff --git a/src/project_layout.rs b/src/project_layout.rs
index 0852d5459..e10a3f33f 100644
--- a/src/project_layout.rs
+++ b/src/project_layout.rs
@@ -175,8 +175,16 @@ impl ProjectResolver {
                 project_root.join(data)
             }
         });
-        let project_layout =
-            ProjectLayout::determine(project_root, extension_name, py_root, python_packages, data)?;
+        let custom_python_source = pyproject.and_then(|x| x.python_source()).is_some();
+        let project_layout = ProjectLayout::determine(
+            project_root,
+            extension_name,
+            py_root,
+            python_packages,
+            data,
+            custom_python_source,
+        )?;
+
         Ok(Self {
             project_layout,
             cargo_toml_path: manifest_file,
@@ -333,15 +341,15 @@ impl ProjectResolver {
 impl ProjectLayout {
     /// Checks whether a python module exists besides Cargo.toml with the right name
     fn determine(
-        project_root: impl AsRef<Path>,
+        project_root: &Path,
         module_name: &str,
         python_root: PathBuf,
         python_packages: Vec<String>,
         data: Option<PathBuf>,
+        custom_python_source: bool,
     ) -> Result<ProjectLayout> {
         // A dot in the module name means the extension module goes into the module folder specified by the path
         let parts: Vec<&str> = module_name.split('.').collect();
-        let project_root = project_root.as_ref();
         let (python_module, rust_module, extension_name) = if parts.len() > 1 {
             let mut rust_module = python_root.clone();
             rust_module.extend(&parts[0..parts.len() - 1]);
@@ -363,6 +371,7 @@ impl ProjectLayout {
             rust_module = %rust_module.display(),
             python_module = %python_module.display(),
             extension_name = %extension_name,
+            module_name = %module_name,
             "Project layout resolved"
         );
 
@@ -395,6 +404,15 @@ impl ProjectLayout {
                 data,
             })
         } else {
+            if custom_python_source {
+                eprintln!(
+                    "⚠️ Warning: You specified the python source as {}, but the python module at \
+                    {} is missing. No python module will be included.",
+                    python_root.display(),
+                    python_module.display()
+                );
+            }
+
             Ok(ProjectLayout {
                 python_dir: python_root,
                 python_packages,
diff --git a/test-crates/wrong-python-source/Cargo.lock b/test-crates/wrong-python-source/Cargo.lock
new file mode 100644
index 000000000..b60250be6
--- /dev/null
+++ b/test-crates/wrong-python-source/Cargo.lock
@@ -0,0 +1,7 @@
+# This file is automatically @generated by Cargo.
+# It is not intended for manual editing.
+version = 3
+
+[[package]]
+name = "wrong-python-source"
+version = "0.1.0"
diff --git a/test-crates/wrong-python-source/Cargo.toml b/test-crates/wrong-python-source/Cargo.toml
new file mode 100644
index 000000000..855bd8413
--- /dev/null
+++ b/test-crates/wrong-python-source/Cargo.toml
@@ -0,0 +1,9 @@
+[package]
+name = "wrong-python-source"
+version = "0.1.0"
+edition = "2021"
+
+[[bin]]
+name = "run_this"
+
+[dependencies]
diff --git a/test-crates/wrong-python-source/pyproject.toml b/test-crates/wrong-python-source/pyproject.toml
new file mode 100644
index 000000000..6559419d5
--- /dev/null
+++ b/test-crates/wrong-python-source/pyproject.toml
@@ -0,0 +1,7 @@
+[tool.maturin]
+bindings = "bin"
+python-source = "python"
+
+[build-system]
+requires = ["maturin>=0.15,<0.16"]
+build-backend = "maturin"
diff --git a/test-crates/wrong-python-source/python/run_this/__init__.py b/test-crates/wrong-python-source/python/run_this/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/test-crates/wrong-python-source/src/bin/run_this.rs b/test-crates/wrong-python-source/src/bin/run_this.rs
new file mode 100644
index 000000000..f328e4d9d
--- /dev/null
+++ b/test-crates/wrong-python-source/src/bin/run_this.rs
@@ -0,0 +1 @@
+fn main() {}
diff --git a/test-crates/wrong-python-source/src/lib.rs b/test-crates/wrong-python-source/src/lib.rs
new file mode 100644
index 000000000..8b1378917
--- /dev/null
+++ b/test-crates/wrong-python-source/src/lib.rs
@@ -0,0 +1 @@
+
diff --git a/tests/common/errors.rs b/tests/common/errors.rs
index d1d095492..4d3b38c99 100644
--- a/tests/common/errors.rs
+++ b/tests/common/errors.rs
@@ -3,6 +3,9 @@ use anyhow::{bail, Result};
 use clap::Parser;
 use maturin::BuildOptions;
 use pretty_assertions::assert_eq;
+use std::path::Path;
+use std::process::Command;
+use std::str;
 
 pub fn abi3_without_version() -> Result<()> {
     // The first argument is ignored by clap
@@ -129,3 +132,28 @@ pub fn invalid_manylinux_does_not_panic() -> Result<()> {
 
     Ok(())
 }
+
+/// The user set `python-source` in pyproject.toml, but there is no python module in there
+pub fn warn_on_missing_python_source() -> Result<()> {
+    let output = Command::new(env!("CARGO_BIN_EXE_maturin"))
+        .arg("build")
+        .arg("-m")
+        .arg(
+            Path::new("test-crates")
+                .join("wrong-python-source")
+                .join("Cargo.toml"),
+        )
+        .output()
+        .unwrap();
+    if !output.status.success() {
+        bail!(
+            "Failed to run: {}\n---stdout:\n{}---stderr:\n{}",
+            output.status,
+            str::from_utf8(&output.stdout)?,
+            str::from_utf8(&output.stderr)?
+        );
+    }
+
+    assert!(str::from_utf8(&output.stderr)?.contains("Warning: You specified the python source as"));
+    Ok(())
+}
diff --git a/tests/run.rs b/tests/run.rs
index bbdc4ffac..b71456ec9 100644
--- a/tests/run.rs
+++ b/tests/run.rs
@@ -406,6 +406,11 @@ fn invalid_manylinux_does_not_panic() {
     handle_result(errors::invalid_manylinux_does_not_panic())
 }
 
+#[test]
+fn warn_on_missing_python_source() {
+    handle_result(errors::warn_on_missing_python_source())
+}
+
 #[test]
 #[cfg_attr(not(target_os = "linux"), ignore)]
 fn musl() {