diff --git a/crates/sui-indexer-alt/src/lib.rs b/crates/sui-indexer-alt/src/lib.rs
index 3a7f284952527..124197a2eae02 100644
--- a/crates/sui-indexer-alt/src/lib.rs
+++ b/crates/sui-indexer-alt/src/lib.rs
@@ -66,7 +66,7 @@ pub struct Indexer {
     last_checkpoint: Option<u64>,
 
     /// Optional override of enabled pipelines.
-    enabled_pipelines: BTreeSet<String>,
+    enabled_pipelines: Option<BTreeSet<String>>,
 
     /// Pipelines that have already been registered with the indexer. Used to make sure a pipeline
     /// with the same name isn't added twice.
@@ -150,6 +150,8 @@ impl Indexer {
         let ingestion_service =
             IngestionService::new(ingestion_config, metrics.clone(), cancel.clone())?;
 
+        let enabled_pipelines: BTreeSet<_> = pipeline.into_iter().collect();
+
         Ok(Self {
             db,
             metrics,
@@ -158,7 +160,11 @@ impl Indexer {
             pipeline_config,
             first_checkpoint,
             last_checkpoint,
-            enabled_pipelines: pipeline.into_iter().collect(),
+            enabled_pipelines: if enabled_pipelines.is_empty() {
+                None
+            } else {
+                Some(enabled_pipelines)
+            },
             added_pipelines: BTreeSet::new(),
             cancel,
             first_checkpoint_from_watermark: u64::MAX,
@@ -278,6 +284,13 @@ impl Indexer {
     /// Ingestion will stop after consuming the configured `last_checkpoint`, if one is provided,
     /// or will continue until it tracks the tip of the network.
     pub async fn run(mut self) -> Result<JoinHandle<()>> {
+        if let Some(enabled_pipelines) = &self.enabled_pipelines {
+            ensure!(
+                enabled_pipelines.is_empty(),
+                "Tried to enable pipelines that this indexer does not know about: {enabled_pipelines:#?}",
+            );
+        }
+
         let metrics_handle = self
             .metrics_service
             .run()
@@ -332,9 +345,11 @@ impl Indexer {
             P::NAME,
         );
 
-        if !self.enabled_pipelines.is_empty() && !self.enabled_pipelines.contains(P::NAME) {
-            info!("Skipping pipeline {}", P::NAME);
-            return Ok(None);
+        if let Some(enabled_pipelines) = &mut self.enabled_pipelines {
+            if !enabled_pipelines.remove(P::NAME) {
+                info!("Skipping pipeline {}", P::NAME);
+                return Ok(None);
+            }
         }
 
         let mut conn = self.db.connect().await.context("Failed DB connection")?;