diff --git a/core/src/subgraph/instance_manager.rs b/core/src/subgraph/instance_manager.rs
index 5d0c89ae171..8273b0045cf 100644
--- a/core/src/subgraph/instance_manager.rs
+++ b/core/src/subgraph/instance_manager.rs
@@ -399,7 +399,15 @@ impl<S: SubgraphStore, AC: amp::Client> SubgraphInstanceManager<S, AC> {
         //   when to stop processing them.
         // - Offchain data sources might require processing beyond the end block of
         //   onchain data sources, so the subgraph needs to continue.
-        let max_end_block: Option<BlockNumber> = if data_sources.len() == end_blocks.len() {
+        //
+        // Note: we explicitly check each data source rather than comparing lengths, because
+        // `end_blocks` is a BTreeSet and deduplicates equal values, which would cause the
+        // length comparison to fail when multiple data sources share the same `end_block`.
+        let max_end_block: Option<BlockNumber> = if data_sources.iter().all(|d| {
+            d.as_onchain()
+                .and_then(|d: &C::DataSource| d.end_block())
+                .is_some()
+        }) {
             end_blocks.iter().max().cloned()
         } else {
             None
diff --git a/core/src/subgraph/runner/mod.rs b/core/src/subgraph/runner/mod.rs
index 1fced161f18..1a6efbc1d6c 100644
--- a/core/src/subgraph/runner/mod.rs
+++ b/core/src/subgraph/runner/mod.rs
@@ -555,11 +555,18 @@ where
                 .observe(block.trigger_count() as f64);
         }
 
-        // Check if we should skip this block (optimization for blocks without triggers)
+        // Check if we should skip this block (optimization for blocks without triggers).
+        // Do not skip if max_end_block has been reached — fall through to process_block so the
+        // block pointer is persisted and the existing max_end_block check in handle_action fires.
+        let max_end_block_reached = self
+            .inputs
+            .max_end_block
+            .is_some_and(|max| block_ptr.number >= max);
         if block.trigger_count() == 0
             && self.state.skip_ptr_updates_timer.elapsed() <= SKIP_PTR_UPDATES_THRESHOLD
             && !self.inputs.store.is_deployment_synced()
             && !close_to_chain_head(&block_ptr, &self.inputs.chain.chain_head_ptr().await?, 1000)
+            && !max_end_block_reached
         {
             // Skip this block and continue with the same stream
             return Ok(RunnerState::AwaitingBlock { block_stream });