diff --git a/src/module_writer/sdist_writer.rs b/src/module_writer/sdist_writer.rs
index 4aa4bdade..b8245194b 100644
--- a/src/module_writer/sdist_writer.rs
+++ b/src/module_writer/sdist_writer.rs
@@ -10,6 +10,7 @@ use flate2::write::GzEncoder;
 use fs_err as fs;
 use ignore::overrides::Override;
 use normpath::PathExt as _;
+use tracing::debug;
 
 use crate::Metadata24;
 
@@ -34,6 +35,7 @@ pub struct SDistWriter {
     file_tracker: FileTracker,
     excludes: Override,
     mtime: u64,
+    target_exclusion_warning_emitted: bool,
 }
 
 impl ModuleWriter for SDistWriter {
@@ -52,6 +54,15 @@ impl ModuleWriter for SDistWriter {
 
         let target = target.as_ref();
         if self.exclude(target) {
+            if !self.target_exclusion_warning_emitted {
+                self.target_exclusion_warning_emitted = true;
+                eprintln!(
+                    "⚠️ Warning: A file was excluded from the archive by the target path in the archive\n\
+                     ⚠️ instead of the source path on the filesystem. This behavior is deprecated and\n\
+                     ⚠️ will be removed in future versions of maturin.",
+                );
+            }
+            debug!("Excluded file {target:?} from archive by target path");
             return Ok(());
         }
 
@@ -110,6 +121,7 @@ impl SDistWriter {
             file_tracker: FileTracker::default(),
             excludes,
             mtime: mtime_override.unwrap_or(SDIST_DETERMINISTIC_TIMESTAMP),
+            target_exclusion_warning_emitted: false,
         })
     }
 
diff --git a/src/module_writer/wheel_writer.rs b/src/module_writer/wheel_writer.rs
index 674841c94..fc92443fc 100644
--- a/src/module_writer/wheel_writer.rs
+++ b/src/module_writer/wheel_writer.rs
@@ -30,6 +30,7 @@ pub struct WheelWriter {
     file_tracker: FileTracker,
     excludes: Override,
     file_options: SimpleFileOptions,
+    target_exclusion_warning_emitted: bool,
 }
 
 impl ModuleWriter for WheelWriter {
@@ -40,8 +41,23 @@ impl ModuleWriter for WheelWriter {
         mut data: impl Read,
         executable: bool,
     ) -> Result<()> {
+        if let Some(source) = source {
+            if self.exclude(source) {
+                return Ok(());
+            }
+        }
+
         let target = target.as_ref();
         if self.exclude(target) {
+            if !self.target_exclusion_warning_emitted {
+                self.target_exclusion_warning_emitted = true;
+                eprintln!(
+                    "⚠️ Warning: A file was excluded from the archive by the target path in the archive\n\
+                     ⚠️ instead of the source path on the filesystem. This behavior is deprecated and\n\
+                     ⚠️ will be removed in future versions of maturin.",
+                );
+            }
+            debug!("Excluded file {target:?} from archive by target path");
             return Ok(());
         }
 
@@ -94,6 +110,7 @@ impl WheelWriter {
             file_tracker: FileTracker::default(),
             excludes,
             file_options,
+            target_exclusion_warning_emitted: false,
         };
 
         write_dist_info(&mut builder, pyproject_dir, metadata24, tags)?;