diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6b0bf5d3..b2bf0241 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -56,6 +56,8 @@ Versioning](https://semver.org/spec/v2.0.0.html).
   lead to a number of surprises. Yabridgectl will now print a warning upon
   syncing when using the symlink installation method, and the feature will be
   removed completely in yabridge 4.0.
+- Blacklisted symlinks and files contained within symlinked directories are now
+  handled correctly when syncing.
 
 ### Packaging notes
 
diff --git a/tools/yabridgectl/src/files.rs b/tools/yabridgectl/src/files.rs
index 398e5e97..d81b1c10 100644
--- a/tools/yabridgectl/src/files.rs
+++ b/tools/yabridgectl/src/files.rs
@@ -348,7 +348,15 @@ pub fn index(directory: &Path, blacklist: &HashSet<&Path>) -> SearchIndex {
     for (file_idx, entry) in WalkDir::new(directory)
         .follow_links(true)
         .into_iter()
-        .filter_entry(|e| !blacklist.contains(e.path()))
+        .filter_entry(|e| {
+            // The blacklist entries are canonicalized to resolve symlinks and to normalize slashes,
+            // so we should do the same thing here as well
+            if let Ok(p) = e.path().canonicalize() {
+                !blacklist.contains(p.as_path())
+            } else {
+                true
+            }
+        })
         .filter_map(|e| e.ok())
         .filter(|e| !e.file_type().is_dir())
         .enumerate()