diff --git a/pixels-cli/src/main/java/io/pixelsdb/pixels/cli/load/IndexedPixelsConsumer.java b/pixels-cli/src/main/java/io/pixelsdb/pixels/cli/load/IndexedPixelsConsumer.java
index 5c7c2b3ad..1c1ff16d0 100644
--- a/pixels-cli/src/main/java/io/pixelsdb/pixels/cli/load/IndexedPixelsConsumer.java
+++ b/pixels-cli/src/main/java/io/pixelsdb/pixels/cli/load/IndexedPixelsConsumer.java
@@ -144,7 +144,8 @@ protected void processSourceFile(String originalFilePath) throws IOException, Me
                  }
              }
          }
-         originStorage.close();
+         // Do not close originStorage: StorageFactory caches one Storage instance per scheme, and the same
+         // instance is used by flushRemainingData() to write the data files when they share the scheme.
      }
 
      @Override
@@ -263,8 +264,6 @@ private void flushRowBatch(PerVirtualNodeWriter bucketWriter) throws IOException
                  queue.clear();
              }
          }
-         bucketWriter.indexService.flushIndexEntriesOfFile(index.getTableId(), index.getId(),
-                 bucketWriter.currFile.getId(), true, bucketWriter.defaultIndexOption);
      }
 
      private void closePixelsFile(PerVirtualNodeWriter bucketWriter) throws IOException, IndexException
@@ -275,6 +274,10 @@ private void closePixelsFile(PerVirtualNodeWriter bucketWriter) throws IOExcepti
              flushRowBatch(bucketWriter);
          }
 
+         // The main index of a file can only be flushed once, hence it is flushed here instead of in flushRowBatch()
+         bucketWriter.indexService.flushIndexEntriesOfFile(index.getTableId(), index.getId(),
+                 bucketWriter.currFile.getId(), true, bucketWriter.defaultIndexOption);
+
          closeWriterAndAddFile(bucketWriter.pixelsWriter, bucketWriter.currFile, bucketWriter.currTargetPath, bucketWriter.targetNode);
      }