diff --git a/crates/sui-indexer-alt/src/lib.rs b/crates/sui-indexer-alt/src/lib.rs
index d558391c0c4e4..8556501733249 100644
--- a/crates/sui-indexer-alt/src/lib.rs
+++ b/crates/sui-indexer-alt/src/lib.rs
@@ -1,8 +1,14 @@
 // Copyright (c) Mysten Labs, Inc.
 // SPDX-License-Identifier: Apache-2.0
 
-use std::{collections::BTreeSet, net::SocketAddr, sync::Arc};
-
+use crate::handlers::ev_emit_mod::EvEmitMod;
+use crate::handlers::ev_struct_inst::EvStructInst;
+use crate::handlers::kv_checkpoints::KvCheckpoints;
+use crate::handlers::kv_objects::KvObjects;
+use crate::handlers::kv_transactions::KvTransactions;
+use crate::handlers::tx_affected_objects::TxAffectedObjects;
+use crate::handlers::tx_balance_changes::TxBalanceChanges;
+use crate::pipeline::PipelineName;
 use anyhow::{Context, Result};
 use db::{Db, DbConfig};
 use handlers::Handler;
@@ -10,6 +16,7 @@ use ingestion::{IngestionConfig, IngestionService};
 use metrics::{IndexerMetrics, MetricsService};
 use models::watermarks::CommitterWatermark;
 use pipeline::{concurrent, PipelineConfig};
+use std::{net::SocketAddr, sync::Arc};
 use task::graceful_shutdown;
 use tokio::task::JoinHandle;
 use tokio_util::sync::CancellationToken;
@@ -47,9 +54,6 @@ pub struct Indexer {
     /// Optional override of the checkpoint upperbound.
     last_checkpoint: Option<u64>,
 
-    /// Optional override of enabled pipelines.
-    enabled_pipelines: BTreeSet<String>,
-
     /// Cancellation token shared among all continuous tasks in the service.
     cancel: CancellationToken,
 
@@ -84,11 +88,6 @@ pub struct IndexerConfig {
     #[arg(long)]
     last_checkpoint: Option<u64>,
 
-    /// Only run the following pipelines -- useful for backfills. If not provided, all pipelines
-    /// will be run.
-    #[arg(long, action = clap::ArgAction::Append)]
-    pipeline: Vec<String>,
-
     /// Address to serve Prometheus Metrics from.
     #[arg(long, default_value = "0.0.0.0:9184")]
     pub metrics_address: SocketAddr,
@@ -102,7 +101,6 @@ impl Indexer {
             pipeline_config,
             first_checkpoint,
             last_checkpoint,
-            pipeline,
             metrics_address,
         } = config;
 
@@ -115,7 +113,7 @@ impl Indexer {
         let ingestion_service =
             IngestionService::new(ingestion_config, metrics.clone(), cancel.clone())?;
 
-        Ok(Self {
+        let mut indexer = Self {
             db,
             metrics,
             metrics_service,
@@ -123,21 +121,35 @@ impl Indexer {
             pipeline_config,
             first_checkpoint,
             last_checkpoint,
-            enabled_pipelines: pipeline.into_iter().collect(),
             cancel,
             first_checkpoint_from_watermark: u64::MAX,
             handles: vec![],
-        })
+        };
+        indexer.register_pipeline().await?;
+        Ok(indexer)
+    }
+
+    async fn register_pipeline(&mut self) -> Result<()> {
+        match self.pipeline_config.pipeline {
+            PipelineName::EvEmitMod => self.concurrent_pipeline::<EvEmitMod>().await?,
+            PipelineName::EvStructInst => self.concurrent_pipeline::<EvStructInst>().await?,
+            PipelineName::KvCheckpoints => self.concurrent_pipeline::<KvCheckpoints>().await?,
+            PipelineName::KvObjects => self.concurrent_pipeline::<KvObjects>().await?,
+            PipelineName::KvTransactions => self.concurrent_pipeline::<KvTransactions>().await?,
+            PipelineName::TxAffectedObjects => {
+                self.concurrent_pipeline::<TxAffectedObjects>().await?
+            }
+            PipelineName::TxBalanceChanges => {
+                self.concurrent_pipeline::<TxBalanceChanges>().await?
+            }
+        }
+
+        Ok(())
     }
 
     /// Adds a new pipeline to this indexer and starts it up. Although their tasks have started,
     /// they will be idle until the ingestion service starts, and serves it checkpoint data.
     pub async fn concurrent_pipeline<H: Handler + 'static>(&mut self) -> Result<()> {
-        if !self.enabled_pipelines.is_empty() && !self.enabled_pipelines.contains(H::NAME) {
-            info!("Skipping pipeline {}", H::NAME);
-            return Ok(());
-        }
-
         let mut conn = self.db.connect().await.context("Failed DB connection")?;
 
         let watermark = CommitterWatermark::get(&mut conn, H::NAME)
diff --git a/crates/sui-indexer-alt/src/main.rs b/crates/sui-indexer-alt/src/main.rs
index 77d90d3fe0cb3..cc8026c3a3548 100644
--- a/crates/sui-indexer-alt/src/main.rs
+++ b/crates/sui-indexer-alt/src/main.rs
@@ -3,15 +3,7 @@
 
 use anyhow::{Context, Result};
 use clap::Parser;
-use sui_indexer_alt::{
-    args::Args,
-    handlers::{
-        ev_emit_mod::EvEmitMod, ev_struct_inst::EvStructInst, kv_checkpoints::KvCheckpoints,
-        kv_objects::KvObjects, kv_transactions::KvTransactions,
-        tx_affected_objects::TxAffectedObjects, tx_balance_changes::TxBalanceChanges,
-    },
-    Indexer,
-};
+use sui_indexer_alt::{args::Args, Indexer};
 use tokio_util::sync::CancellationToken;
 
 #[tokio::main]
@@ -25,15 +17,7 @@ async fn main() -> Result<()> {
 
     let cancel = CancellationToken::new();
 
-    let mut indexer = Indexer::new(args.indexer_config, cancel.clone()).await?;
-
-    indexer.concurrent_pipeline::<EvEmitMod>().await?;
-    indexer.concurrent_pipeline::<EvStructInst>().await?;
-    indexer.concurrent_pipeline::<KvCheckpoints>().await?;
-    indexer.concurrent_pipeline::<KvObjects>().await?;
-    indexer.concurrent_pipeline::<KvTransactions>().await?;
-    indexer.concurrent_pipeline::<TxAffectedObjects>().await?;
-    indexer.concurrent_pipeline::<TxBalanceChanges>().await?;
+    let indexer = Indexer::new(args.indexer_config, cancel.clone()).await?;
 
     let h_indexer = indexer.run().await.context("Failed to start indexer")?;
 
diff --git a/crates/sui-indexer-alt/src/pipeline/mod.rs b/crates/sui-indexer-alt/src/pipeline/mod.rs
index 12893179676da..174b55eef6447 100644
--- a/crates/sui-indexer-alt/src/pipeline/mod.rs
+++ b/crates/sui-indexer-alt/src/pipeline/mod.rs
@@ -1,9 +1,8 @@
 // Copyright (c) Mysten Labs, Inc.
 // SPDX-License-Identifier: Apache-2.0
 
-use std::time::Duration;
-
 use crate::{handlers::Handler, models::watermarks::CommitterWatermark};
+use std::time::Duration;
 
 pub mod concurrent;
 mod processor;
@@ -14,6 +13,8 @@ const COMMITTER_BUFFER: usize = 5;
 
 #[derive(clap::Args, Debug, Clone)]
 pub struct PipelineConfig {
+    #[command(subcommand)]
+    pub pipeline: PipelineName,
     /// Committer will check for pending data at least this often
     #[arg(
         long,
@@ -37,6 +38,18 @@ pub struct PipelineConfig {
     skip_watermark: bool,
 }
 
+/// Each enum variant can also take pipeline-specific configuration.
+#[derive(Debug, Clone, clap::Subcommand)]
+pub enum PipelineName {
+    EvEmitMod,
+    EvStructInst,
+    KvCheckpoints,
+    KvObjects,
+    KvTransactions,
+    TxAffectedObjects,
+    TxBalanceChanges,
+}
+
 /// A batch of processed values associated with a single checkpoint. This is an internal type used
 /// to communicate between the handler and the committer parts of the pipeline.
 struct Indexed<H: Handler> {