diff --git a/core/sail/nativerdf/src/main/java/org/eclipse/rdf4j/sail/nativerdf/btree/BTree.java b/core/sail/nativerdf/src/main/java/org/eclipse/rdf4j/sail/nativerdf/btree/BTree.java
index bcf91f5139..b297d940ea 100644
--- a/core/sail/nativerdf/src/main/java/org/eclipse/rdf4j/sail/nativerdf/btree/BTree.java
+++ b/core/sail/nativerdf/src/main/java/org/eclipse/rdf4j/sail/nativerdf/btree/BTree.java
@@ -25,6 +25,7 @@
 import org.eclipse.rdf4j.common.io.ByteArrayUtil;
 import org.eclipse.rdf4j.common.io.NioFile;
 import org.eclipse.rdf4j.sail.SailException;
+import org.eclipse.rdf4j.sail.nativerdf.NativeStore;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -292,9 +293,10 @@ public BTree(File dataDir, String filenamePrefix, int blockSize, int valueSize,
 			this.valueSize = buf.getInt();
 			this.rootNodeID = buf.getInt();
 
-			if (rootNodeID == 0) {
-				if (nioFile.size() >= 1024) {
-					throw new IllegalStateException("Root node ID is 0 but file is not empty");
+			if (rootNodeID == 0 && NativeStore.SOFT_FAIL_ON_CORRUPT_DATA_AND_REPAIR_INDEXES) {
+				if (nioFile.size() > blockSize) {
+					throw new SailException("Root node ID is 0 but file is not empty. Btree may be corrupt. File: "
+							+ file.getAbsolutePath());
 				}
 			}