diff --git a/crates/dump/src/reader/mod.rs b/crates/dump/src/reader/mod.rs
index f2a8ac90c..53ff4844c 100644
--- a/crates/dump/src/reader/mod.rs
+++ b/crates/dump/src/reader/mod.rs
@@ -232,7 +232,11 @@ pub(crate) mod test {
     use std::{fs::File, io::Seek};
 
     use meili_snap::insta;
-    use meilisearch_types::{batches::{Batch, BatchEnqueuedAt, BatchStats}, task_view::DetailsView, tasks::{BatchStopReason, Kind, Status}};
+    use meilisearch_types::{
+        batches::{Batch, BatchEnqueuedAt, BatchStats},
+        task_view::DetailsView,
+        tasks::{BatchStopReason, Kind, Status},
+    };
     use time::macros::datetime;
 
     use super::*;
diff --git a/crates/index-scheduler/src/queue/batches.rs b/crates/index-scheduler/src/queue/batches.rs
index b96f65836..62f145730 100644
--- a/crates/index-scheduler/src/queue/batches.rs
+++ b/crates/index-scheduler/src/queue/batches.rs
@@ -66,7 +66,7 @@ impl BatchQueue {
         NUMBER_OF_DATABASES
     }
 
-    pub(super) fn new(env: &Env<WithoutTls>, wtxn: &mut RwTxn) -> Result<Self> {
+    pub(crate) fn new(env: &Env<WithoutTls>, wtxn: &mut RwTxn) -> Result<Self> {
         Ok(Self {
             all_batches: env.create_database(wtxn, Some(db_name::ALL_BATCHES))?,
             status: env.create_database(wtxn, Some(db_name::BATCH_STATUS))?,
diff --git a/crates/index-scheduler/src/queue/mod.rs b/crates/index-scheduler/src/queue/mod.rs
index 92de10fe1..1d90cddaa 100644
--- a/crates/index-scheduler/src/queue/mod.rs
+++ b/crates/index-scheduler/src/queue/mod.rs
@@ -32,7 +32,7 @@ use crate::{Error, IndexSchedulerOptions, Result, TaskId};
 /// The number of database used by queue itself
 const NUMBER_OF_DATABASES: u32 = 1;
 /// Database const names for the `IndexScheduler`.
-mod db_name {
+pub(crate) mod db_name {
     pub const BATCH_TO_TASKS_MAPPING: &str = "batch-to-tasks-mapping";
 }
 
diff --git a/crates/index-scheduler/src/upgrade/mod.rs b/crates/index-scheduler/src/upgrade/mod.rs
index a749b31d5..69c91b642 100644
--- a/crates/index-scheduler/src/upgrade/mod.rs
+++ b/crates/index-scheduler/src/upgrade/mod.rs
@@ -7,6 +7,9 @@ use tracing::info;
 
 use crate::queue::TaskQueue;
 use crate::versioning::Versioning;
+use v1_18::V1_17_To_V1_18_0;
+
+mod v1_18;
 
 trait UpgradeIndexScheduler {
     fn upgrade(
@@ -29,7 +32,8 @@ pub fn upgrade_index_scheduler(
     let current_patch = to.2;
 
     let upgrade_functions: &[&dyn UpgradeIndexScheduler] = &[
-        // This is the last upgrade function, it will be called when the index is up to date.
+        &V1_17_To_V1_18_0 {},
+        // This is the last upgrade function, it will be called when the scheduler is up to date.
         // any other upgrade function should be added before this one.
         &ToCurrentNoOp {},
     ];
@@ -40,6 +44,7 @@ pub fn upgrade_index_scheduler(
         (1, 14, _) => 0,
         (1, 15, _) => 0,
         (1, 16, _) => 0,
+        (1, 17, _) => 0,
         (major, minor, patch) => {
             if major > current_major
                 || (major == current_major && minor > current_minor)
diff --git a/crates/index-scheduler/src/upgrade/v1_18.rs b/crates/index-scheduler/src/upgrade/v1_18.rs
new file mode 100644
index 000000000..65909cdb3
--- /dev/null
+++ b/crates/index-scheduler/src/upgrade/v1_18.rs
@@ -0,0 +1,62 @@
+use meilisearch_types::{
+    heed::Database,
+    milli::{CboRoaringBitmapCodec, BEU32},
+};
+use tracing::info;
+
+use super::UpgradeIndexScheduler;
+use crate::queue::{db_name::BATCH_TO_TASKS_MAPPING, BatchQueue};
+
+#[allow(non_camel_case_types)]
+pub(super) struct V1_17_To_V1_18_0();
+
+impl UpgradeIndexScheduler for V1_17_To_V1_18_0 {
+    fn upgrade(
+        &self,
+        env: &meilisearch_types::heed::Env<meilisearch_types::heed::WithoutTls>,
+        wtxn: &mut meilisearch_types::heed::RwTxn,
+        _original: (u32, u32, u32),
+    ) -> anyhow::Result<()> {
+        let batch_queue = BatchQueue::new(env, wtxn)?;
+        let all_batch_ids = batch_queue.all_batch_ids(wtxn)?;
+
+        let batch_to_tasks_mapping: Database<BEU32, CboRoaringBitmapCodec> =
+            env.create_database(wtxn, Some(BATCH_TO_TASKS_MAPPING))?;
+
+        let all_batches = batch_queue.all_batches.lazily_decode_data();
+        let iter = all_batches.iter(wtxn)?;
+        let mut range_start = None;
+        let mut count = 0;
+        let mut ranges = Vec::new();
+        for batch in iter {
+            let (batch_id, _) = batch?;
+
+            if !all_batch_ids.contains(batch_id) {
+                count += 1;
+                if range_start.is_none() {
+                    range_start = Some(batch_id);
+                }
+            } else if let Some(start) = range_start.take() {
+                ranges.push(start..batch_id);
+            }
+        }
+        if let Some(start) = range_start {
+            ranges.push(start..u32::MAX);
+        }
+
+        if !ranges.is_empty() {
+            info!("Removing {count} batches that were not properly removed in previous versions due to #5827.");
+        }
+
+        for range in ranges {
+            batch_queue.all_batches.delete_range(wtxn, &range)?;
+            batch_to_tasks_mapping.delete_range(wtxn, &range)?;
+        }
+
+        Ok(())
+    }
+
+    fn target_version(&self) -> (u32, u32, u32) {
+        (1, 18, 0)
+    }
+}