diff --git a/snix/castore/src/directoryservice/redb.rs b/snix/castore/src/directoryservice/redb.rs
index 2eaa0b515..973ac5f1a 100644
--- a/snix/castore/src/directoryservice/redb.rs
+++ b/snix/castore/src/directoryservice/redb.rs
@@ -3,7 +3,7 @@ use prost::Message;
 use redb::{Database, TableDefinition};
 use std::{path::PathBuf, sync::Arc};
 use tonic::async_trait;
-use tracing::{instrument, warn};
+use tracing::{info, instrument, warn};
 
 use super::{
     Directory, DirectoryGraph, DirectoryPutter, DirectoryService, LeavesToRootValidator,
@@ -41,7 +41,15 @@ impl RedbDirectoryService {
         }
 
         let db = tokio::task::spawn_blocking(|| -> Result<_, redb::Error> {
-            let db = redb::Database::create(path)?;
+            let mut db = redb::Database::builder()
+                .create_with_file_format_v3(true)
+                .create(path)?;
+
+            // Upgrade redb database file format.
+            if db.upgrade()? {
+                info!("Upgraded database format");
+            };
+
             create_schema(&db)?;
             Ok(db)
         })
@@ -55,8 +63,9 @@ impl RedbDirectoryService {
 
     /// Constructs a new instance using the in-memory backend.
     pub fn new_temporary() -> Result<Self, Error> {
-        let db =
-            redb::Database::builder().create_with_backend(redb::backends::InMemoryBackend::new())?;
+        let db = redb::Database::builder()
+            .create_with_file_format_v3(true)
+            .create_with_backend(redb::backends::InMemoryBackend::new())?;
 
         create_schema(&db)?;
 
diff --git a/snix/castore/src/errors.rs b/snix/castore/src/errors.rs
index 84567fbc3..282ce0097 100644
--- a/snix/castore/src/errors.rs
+++ b/snix/castore/src/errors.rs
@@ -125,6 +125,12 @@ impl From<redb::CommitError> for Error {
     }
 }
 
+impl From<redb::UpgradeError> for Error {
+    fn from(value: redb::UpgradeError) -> Self {
+        Error::StorageError(value.to_string())
+    }
+}
+
 impl From<std::io::Error> for Error {
     fn from(value: std::io::Error) -> Self {
         if value.kind() == std::io::ErrorKind::InvalidInput {
diff --git a/snix/store/src/pathinfoservice/redb.rs b/snix/store/src/pathinfoservice/redb.rs
index 851145817..3cd1adff9 100644
--- a/snix/store/src/pathinfoservice/redb.rs
+++ b/snix/store/src/pathinfoservice/redb.rs
@@ -11,7 +11,7 @@ use snix_castore::{
 use std::{path::PathBuf, sync::Arc};
 use tokio_stream::wrappers::ReceiverStream;
 use tonic::async_trait;
-use tracing::{instrument, warn};
+use tracing::{info, instrument, warn};
 
 const PATHINFO_TABLE: TableDefinition<[u8; 20], Vec<u8>> = TableDefinition::new("pathinfo");
 
@@ -40,7 +40,15 @@ impl RedbPathInfoService {
         }
 
         let db = tokio::task::spawn_blocking(|| -> Result<_, redb::Error> {
-            let db = redb::Database::create(path)?;
+            let mut db = redb::Database::builder()
+                .create_with_file_format_v3(true)
+                .create(path)?;
+
+            // Upgrade redb database file format.
+            if db.upgrade()? {
+                info!("Upgraded database format");
+            };
+
             create_schema(&db)?;
             Ok(db)
         })
@@ -54,8 +62,9 @@ impl RedbPathInfoService {
 
     /// Constructs a new instance using the in-memory backend.
     pub fn new_temporary(instance_name: String) -> Result<Self, Error> {
-        let db =
-            redb::Database::builder().create_with_backend(redb::backends::InMemoryBackend::new())?;
+        let db = redb::Database::builder()
+            .create_with_file_format_v3(true)
+            .create_with_backend(redb::backends::InMemoryBackend::new())?;
 
         create_schema(&db)?;