diff --git a/docs/configuration/source-config.md b/docs/configuration/source-config.md
index 83bdace6f96..d00157ead0b 100644
--- a/docs/configuration/source-config.md
+++ b/docs/configuration/source-config.md
@@ -56,6 +56,8 @@ Required fields for the SQS `notifications` parameter items:
 - `message_type`: format of the message payload, either
   - `s3_notification`: an [S3 event notification](https://docs.aws.amazon.com/AmazonS3/latest/userguide/EventNotifications.html)
   - `raw_uri`: a message containing just the file object URI (e.g. `s3://mybucket/mykey`)
+  - `deduplication_window_duration_sec`: maximum duration for which ingested files checkpoints are kept (default 3600)
+  - `deduplication_window_max_messages`: maximum number of ingested file checkpoints kept (default 100k)
 
 *Adding a file source with SQS notifications to an index with the [CLI](../reference/cli.md#source)*
 
@@ -82,6 +84,7 @@ EOF
   - the notification message could not be parsed (e.g it is not a valid S3 notification)
   - the file was not found
   - the file is corrupted (e.g unexpected compression)
+- AWS S3 notifications and AWS SQS provide "at least once" delivery guaranties. To avoid duplicates, the file source includes a mechanism that prevents the same file from being ingested twice. It works by storing checkpoints in the metastore that track the indexing progress for each file. You can decrease `deduplication_window_duration_sec` and/or `deduplication_window_max_messages` to reduce the load on the metastore.
 
 :::
 
diff --git a/quickwit/quickwit-config/src/source_config/mod.rs b/quickwit/quickwit-config/src/source_config/mod.rs
index b9fcaa15018..8fc7583735f 100644
--- a/quickwit/quickwit-config/src/source_config/mod.rs
+++ b/quickwit/quickwit-config/src/source_config/mod.rs
@@ -264,6 +264,18 @@ pub enum FileSourceMessageType {
 pub struct FileSourceSqs {
     pub queue_url: String,
     pub message_type: FileSourceMessageType,
+    #[serde(default = "default_deduplication_window_duration_sec")]
+    pub deduplication_window_duration_sec: u32,
+    #[serde(default = "default_deduplication_window_max_messages")]
+    pub deduplication_window_max_messages: u32,
+}
+
+fn default_deduplication_window_duration_sec() -> u32 {
+    3600
+}
+
+fn default_deduplication_window_max_messages() -> u32 {
+    100_000
 }
 
 #[derive(Clone, Debug, Eq, PartialEq, Serialize, Deserialize, utoipa::ToSchema)]
@@ -891,12 +903,20 @@ mod tests {
                     queue_url: "https://sqs.us-east-1.amazonaws.com/123456789012/queue-name"
                         .to_string(),
                     message_type: FileSourceMessageType::S3Notification,
+                    deduplication_window_duration_sec: default_deduplication_window_duration_sec(),
+                    deduplication_window_max_messages: default_deduplication_window_max_messages(),
                 })),
             );
             let file_params_reserialized = serde_json::to_value(&file_params_deserialized).unwrap();
             assert_eq!(
                 file_params_reserialized,
-                json!({"notifications": [{"type": "sqs", "queue_url": "https://sqs.us-east-1.amazonaws.com/123456789012/queue-name", "message_type": "s3_notification"}]})
+                json!({"notifications": [{
+                    "type": "sqs",
+                    "queue_url": "https://sqs.us-east-1.amazonaws.com/123456789012/queue-name",
+                    "message_type": "s3_notification",
+                    "deduplication_window_duration_sec": default_deduplication_window_duration_sec(),
+                    "deduplication_window_max_messages": default_deduplication_window_max_messages()
+                }]})
             );
         }
         {
diff --git a/quickwit/quickwit-indexing/src/source/file_source.rs b/quickwit/quickwit-indexing/src/source/file_source.rs
index e3be553ae1b..a339f7cd677 100644
--- a/quickwit/quickwit-indexing/src/source/file_source.rs
+++ b/quickwit/quickwit-indexing/src/source/file_source.rs
@@ -435,6 +435,8 @@ mod localstack_tests {
             FileSourceParams::Notifications(FileSourceNotification::Sqs(FileSourceSqs {
                 queue_url,
                 message_type: FileSourceMessageType::RawUri,
+                deduplication_window_duration_sec: 100,
+                deduplication_window_max_messages: 100,
             }));
         let source_config = SourceConfig::for_test(
             "test-file-source-sqs-notifications",
diff --git a/quickwit/quickwit-indexing/src/source/queue_sources/coordinator.rs b/quickwit/quickwit-indexing/src/source/queue_sources/coordinator.rs
index 0d52ce8352c..459edfbb3f4 100644
--- a/quickwit/quickwit-indexing/src/source/queue_sources/coordinator.rs
+++ b/quickwit/quickwit-indexing/src/source/queue_sources/coordinator.rs
@@ -96,6 +96,8 @@ impl QueueCoordinator {
         source_runtime: SourceRuntime,
         queue: Arc<dyn Queue>,
         message_type: MessageType,
+        shard_max_age: Option<u32>,
+        shard_max_count: Option<u32>,
     ) -> Self {
         Self {
             shared_state: QueueSharedState {
@@ -106,8 +108,8 @@ impl QueueCoordinator {
                     2 * source_runtime.indexing_setting.commit_timeout_secs as u64,
                 ),
                 last_initiated_pruning: Instant::now(),
-                max_age: None,
-                max_count: None,
+                max_age: shard_max_age,
+                max_count: shard_max_count,
                 pruning_interval: Duration::from_secs(60),
             },
             local_state: QueueLocalState::default(),
@@ -141,6 +143,8 @@ impl QueueCoordinator {
             source_runtime,
             Arc::new(queue),
             message_type,
+            Some(config.deduplication_window_duration_sec),
+            Some(config.deduplication_window_max_messages),
         ))
     }