diff --git a/rust/lance/src/dataset/optimize.rs b/rust/lance/src/dataset/optimize.rs
index 87dda8e7e57..a0bc5986aac 100644
--- a/rust/lance/src/dataset/optimize.rs
+++ b/rust/lance/src/dataset/optimize.rs
@@ -7316,4 +7316,93 @@ mod tests {
             ]
         );
     }
+
+    // Compaction should materialize a fully-deleted fragment: drop it from both
+    // the index's data and its coverage, so searches stay on the fast path
+    // instead of masking a fragment that no longer exists.
+    #[tokio::test]
+    async fn test_compaction_materializes_deleted_fragment() {
+        let mut data_gen =
+            BatchGenerator::new().col(Box::new(IncrementingInt32::new().named("i".to_owned())));
+        // 10 fragments x 100 rows, i = 0..1000. Fragment 4 holds i in [400,500).
+        let mut dataset = Dataset::write(
+            data_gen.batch(1_000),
+            "memory://test/table",
+            Some(WriteParams {
+                max_rows_per_file: 100,
+                ..Default::default()
+            }),
+        )
+        .await
+        .unwrap();
+        assert_eq!(dataset.get_fragments().len(), 10);
+
+        dataset
+            .create_index(
+                &["i"],
+                IndexType::BTree,
+                Some("i_idx".into()),
+                &ScalarIndexParams::default(),
+                false,
+            )
+            .await
+            .unwrap();
+
+        // Fully delete fragment 4 (removed from the manifest, never compacted).
+        dataset.delete("i >= 400 AND i < 500").await.unwrap();
+        assert_eq!(dataset.get_fragments().len(), 9);
+
+        // Inline compaction (not deferred): indexes are remapped immediately.
+        compact_files(
+            &mut dataset,
+            CompactionOptions {
+                target_rows_per_fragment: 100_000,
+                materialize_deletions: true,
+                defer_index_remap: false,
+                ..Default::default()
+            },
+            None,
+        )
+        .await
+        .unwrap();
+
+        // Coverage: the deleted fragment 4 must be gone, leaving exactly the
+        // live fragments (without the fix, fragment 4 lingers in the bitmap).
+        let index = dataset
+            .load_index_by_name("i_idx")
+            .await
+            .unwrap()
+            .expect("index must exist");
+        let bitmap = index
+            .fragment_bitmap
+            .expect("index must store a fragment bitmap");
+        assert!(
+            !bitmap.contains(4),
+            "deleted fragment 4 still covered by the index: {bitmap:?}"
+        );
+        let live: roaring::RoaringBitmap = dataset
+            .get_fragments()
+            .iter()
+            .map(|f| f.id() as u32)
+            .collect();
+        assert_eq!(
+            bitmap, live,
+            "index coverage should equal the live fragments"
+        );
+
+        // Data: an indexed filtered scan resolves row addresses and takes. If the
+        // deleted fragment's rows survived in the index data while its coverage
+        // was trimmed, this take would error on a missing fragment.
+        let batch = dataset
+            .scan()
+            .filter("i >= 400 AND i < 500")
+            .unwrap()
+            .project(&["i"])
+            .unwrap()
+            .try_into_batch()
+            .await
+            .expect("indexed scan over the deleted range must succeed");
+        assert_eq!(batch.num_rows(), 0, "deleted fragment rows resurfaced");
+        assert_eq!(dataset.count_rows(None).await.unwrap(), 900);
+    }
 }
diff --git a/rust/lance/src/dataset/transaction.rs b/rust/lance/src/dataset/transaction.rs
index 4555cd7ee6c..7548df83843 100644
--- a/rust/lance/src/dataset/transaction.rs
+++ b/rust/lance/src/dataset/transaction.rs
@@ -2070,17 +2070,27 @@ impl Transaction {
                     next_row_id.as_ref(),
                 )?;
 
+                let live_fragments: RoaringBitmap =
+                    final_fragments.iter().map(|f| f.id as u32).collect();
                 if next_row_id.is_some() {
                     // We can re-use indices, but need to rewrite the fragment bitmaps
                     debug_assert!(rewritten_indices.is_empty());
                     for index in final_indices.iter_mut() {
                         if let Some(fragment_bitmap) = &mut index.fragment_bitmap {
-                            *fragment_bitmap =
-                                Self::recalculate_fragment_bitmap(fragment_bitmap, groups)?;
+                            *fragment_bitmap = Self::recalculate_fragment_bitmap(
+                                fragment_bitmap,
+                                groups,
+                                &live_fragments,
+                            )?;
                         }
                     }
                 } else {
-                    Self::handle_rewrite_indices(&mut final_indices, rewritten_indices, groups)?;
+                    Self::handle_rewrite_indices(
+                        &mut final_indices,
+                        rewritten_indices,
+                        groups,
+                        &live_fragments,
+                    )?;
                 }
 
                 if let Some(frag_reuse_index) = frag_reuse_index {
@@ -2744,6 +2754,7 @@ impl Transaction {
     fn recalculate_fragment_bitmap(
         old: &RoaringBitmap,
         groups: &[RewriteGroup],
+        live_fragments: &RoaringBitmap,
     ) -> Result<RoaringBitmap> {
         let mut new_bitmap = old.clone();
         for group in groups {
@@ -2772,6 +2783,12 @@ impl Transaction {
                 }
             }
         }
+        // Drop fragments that are no longer in the dataset (fully deleted before
+        // this compaction). They were never part of a rewrite group, so the loop
+        // above leaves them in coverage; trimming them here keeps index searches
+        // on the fast path. The corresponding index data is dropped during the
+        // remap (see index::deleted_fragment_row_id_drops).
+        new_bitmap &= live_fragments;
         Ok(new_bitmap)
     }
 
@@ -2779,6 +2796,7 @@ impl Transaction {
         indices: &mut [IndexMetadata],
         rewritten_indices: &[RewrittenIndex],
         groups: &[RewriteGroup],
+        live_fragments: &RoaringBitmap,
     ) -> Result<()> {
         let mut modified_indices = HashSet::new();
 
@@ -2806,6 +2824,7 @@ impl Transaction {
                     ))
                 })?,
                 groups,
+                live_fragments,
             )?);
             index.uuid = rewritten_index.new_id;
             // Update file sizes to match the new index files. When not available
@@ -4816,7 +4835,12 @@ mod tests {
         }];
 
         // Should succeed (skip missing index) instead of error
-        let result = Transaction::handle_rewrite_indices(&mut indices, &rewritten_indices, &[]);
+        let result = Transaction::handle_rewrite_indices(
+            &mut indices,
+            &rewritten_indices,
+            &[],
+            &RoaringBitmap::new(),
+        );
         assert!(result.is_ok());
         assert!(indices.is_empty());
     }
diff --git a/rust/lance/src/index.rs b/rust/lance/src/index.rs
index 1a3a3aa54ec..01cdb878675 100644
--- a/rust/lance/src/index.rs
+++ b/rust/lance/src/index.rs
@@ -474,6 +474,46 @@ pub trait IndexBuilder {
     async fn build(&self) -> Result<()>;
 }
 
+/// `addr -> None` drops for every row of a fragment this index still covers
+/// that is no longer in the dataset (fully deleted before compaction). The
+/// fragments are gone from the current manifest, so their rows are enumerated
+/// from the dataset version the index was built at. Returns `None` if that
+/// version can't be loaded (e.g. already cleaned up), leaving those rows to
+/// query-time masking as before.
+async fn deleted_fragment_row_id_drops(
+    dataset: &Dataset,
+    index: &IndexMetadata,
+) -> Result<Option<HashMap<u64, Option<u64>>>> {
+    let Some(coverage) = index.fragment_bitmap.as_ref() else {
+        return Ok(None);
+    };
+    let live: RoaringBitmap = dataset
+        .get_fragments()
+        .iter()
+        .map(|f| f.id() as u32)
+        .collect();
+    let dead = coverage - &live;
+    if dead.is_empty() {
+        return Ok(None);
+    }
+    let Ok(old) = dataset.checkout_version(index.dataset_version).await else {
+        return Ok(None);
+    };
+    let mut drops = HashMap::new();
+    for frag in old.get_fragments() {
+        let fid = frag.id() as u32;
+        if !dead.contains(fid) {
+            continue;
+        }
+        if let Some(rows) = frag.metadata().physical_rows {
+            for offset in 0..rows as u32 {
+                drops.insert(u64::from(RowAddress::new_from_parts(fid, offset)), None);
+            }
+        }
+    }
+    Ok(Some(drops))
+}
+
 pub(crate) async fn remap_index(
     dataset: &Dataset,
     index_id: &Uuid,
@@ -492,6 +532,25 @@ pub(crate) async fn remap_index(
         ));
     }
 
+    // Materialize fully-deleted fragments. A fragment deleted before this
+    // compaction is gone from the manifest but may still be covered by this
+    // index: it was never part of a rewrite group, so its rows are absent from
+    // `row_id_map` and would survive the rebuild, keeping the index's coverage
+    // pinned to a fragment that no longer exists and forcing searches onto the
+    // masked slow path. Map every such row to None so it is dropped from the
+    // rebuilt index; coverage is trimmed to match at commit time (see
+    // Transaction::recalculate_fragment_bitmap).
+    let augmented_map;
+    let row_id_map = match deleted_fragment_row_id_drops(dataset, matched).await? {
+        Some(extra) if !extra.is_empty() => {
+            let mut m = row_id_map.clone();
+            m.extend(extra);
+            augmented_map = m;
+            &augmented_map
+        }
+        _ => row_id_map,
+    };
+
     if row_id_map.values().all(|v| v.is_none()) {
         let deleted_bitmap = RoaringBitmap::from_iter(
             row_id_map