diff --git a/src/rust/engine/options/src/lib.rs b/src/rust/engine/options/src/lib.rs
index 47400d05ec2..801a0a14aff 100644
--- a/src/rust/engine/options/src/lib.rs
+++ b/src/rust/engine/options/src/lib.rs
@@ -489,19 +489,30 @@ impl OptionParser {
             }
             derivation = Some(derivations);
         }
+
+        // Removals from any source apply after adds from any source (but are themselves
+        // overridden by later replacements), so we collect them here and apply them later.
+        let mut removal_lists: Vec<Vec<T>> = vec![];
+
         let mut highest_priority_source = Source::Default;
         for (source_type, source) in self.sources.iter() {
             if let Some(list_edits) = getter(source, id)? {
                 highest_priority_source = source_type.clone();
                 for list_edit in list_edits {
                     match list_edit.action {
-                        ListEditAction::Replace => list = list_edit.items,
+                        ListEditAction::Replace => {
+                            list = list_edit.items;
+                            removal_lists.clear();
+                        }
                         ListEditAction::Add => list.extend(list_edit.items),
-                        ListEditAction::Remove => remover(&mut list, &list_edit.items),
+                        ListEditAction::Remove => removal_lists.push(list_edit.items),
                     }
                 }
             }
         }
+        for removals in removal_lists {
+            remover(&mut list, &removals);
+        }
         Ok(ListOptionValue {
             derivation,
             source: highest_priority_source,
diff --git a/src/rust/engine/options/src/tests.rs b/src/rust/engine/options/src/tests.rs
index 2de7ba1ace5..eb2e2e5e367 100644
--- a/src/rust/engine/options/src/tests.rs
+++ b/src/rust/engine/options/src/tests.rs
@@ -280,7 +280,7 @@ fn test_parse_list_options() {
     );
 
     check(
-        vec![1, 3, 4],
+        vec![1, 3],
         vec![
             (Source::Default, vec![replace(vec![0])]),
             (config_source(), vec![replace(vec![1, 2])]),
@@ -290,7 +290,7 @@ fn test_parse_list_options() {
         vec![],
         vec![("PANTS_SCOPE_FOO", "+[3, 4]")],
         "[scope]\nfoo = [1, 2]",
-        "[scope]\nfoo = '-[2, 4]'", // 2 should be removed, but not 4, since env has precedence.
+        "[scope]\nfoo = '-[2, 4]'",
     );
 
     check(
@@ -330,6 +330,63 @@ fn test_parse_list_options() {
         "",
         "",
     );
+
+    // Filtering all instances of repeated values.
+    check(
+        vec![1, 2, 2, 4],
+        vec![
+            (Source::Default, vec![replace(vec![0])]),
+            (config_source(), vec![add(vec![1, 2, 3, 2, 0, 3, 3, 4])]),
+            (Source::Env, vec![remove(vec![0, 3])]),
+        ],
+        vec![],
+        vec![("PANTS_SCOPE_FOO", "-[0, 3]")],
+        "[scope]\nfoo.add = [1, 2, 3, 2, 0, 3, 3, 4]",
+        "",
+    );
+
+    // Filtering a value even though it was appended again at a higher rank.
+    check(
+        vec![0, 2],
+        vec![
+            (Source::Default, vec![replace(vec![0])]),
+            (config_source(), vec![add(vec![1, 2])]),
+            (Source::Env, vec![remove(vec![1])]),
+            (Source::Flag, vec![add(vec![1])]),
+        ],
+        vec!["--scope-foo=+[1]"],
+        vec![("PANTS_SCOPE_FOO", "-[1]")],
+        "[scope]\nfoo.add = [1, 2]",
+        "",
+    );
+
+    // Filtering a value even though it was appended again at the same rank.
+    check(
+        vec![0, 2],
+        vec![
+            (Source::Default, vec![replace(vec![0])]),
+            (config_source(), vec![add(vec![1, 2])]),
+            (Source::Env, vec![remove(vec![1]), add(vec![1])]),
+        ],
+        vec![],
+        vec![("PANTS_SCOPE_FOO", "-[1],+[1]")],
+        "[scope]\nfoo.add = [1, 2]",
+        "",
+    );
+
+    // Overwriting cancels filters.
+    check(
+        vec![0],
+        vec![
+            (Source::Default, vec![replace(vec![0])]),
+            (config_source(), vec![remove(vec![0])]),
+            (Source::Env, vec![replace(vec![0])]),
+        ],
+        vec![],
+        vec![("PANTS_SCOPE_FOO", "[0]")],
+        "[scope]\nfoo.remove = [0]",
+        "",
+    );
 }
 
 #[test]