diff --git a/src/database/mod.rs b/src/database/mod.rs
index d8c357c..63533dd 100644
--- a/src/database/mod.rs
+++ b/src/database/mod.rs
@@ -238,6 +238,7 @@ pub struct OpenResult {
     pub new: bool,
 }
 
+pub const UPEND_SUBDIR: &str = ".upend";
 pub const DATABASE_FILENAME: &str = "upend.sqlite3";
 
 pub fn open_upend<P: AsRef<Path>>(
@@ -247,16 +248,23 @@ pub fn open_upend<P: AsRef<Path>>(
 ) -> Result<OpenResult> {
     embed_migrations!("./migrations/upend/");
 
-    let database_path = db_path.unwrap_or_else(|| dirpath.as_ref().join(DATABASE_FILENAME));
+    let upend_path = db_path.unwrap_or_else(|| dirpath.as_ref().join(UPEND_SUBDIR));
 
     if reinitialize {
         trace!("Reinitializing - removing previous database...");
-        let _ = fs::remove_file(&database_path);
+        let _ = fs::remove_dir_all(&upend_path);
+    }
+    let new = !upend_path.exists();
+
+    if new {
+        trace!("Creating UpEnd subdirectory...");
+        fs::create_dir(&upend_path)?;
     }
-    let new = !database_path.exists();
 
     trace!("Creating pool.");
-    let manager = ConnectionManager::<SqliteConnection>::new(database_path.to_str().unwrap());
+    let manager = ConnectionManager::<SqliteConnection>::new(
+        upend_path.join(DATABASE_FILENAME).to_str().unwrap(),
+    );
     let pool = r2d2::Pool::builder()
         .connection_customizer(Box::new(ConnectionOptions {
             enable_foreign_keys: true,
diff --git a/src/filesystem.rs b/src/filesystem.rs
index 0dc2479..74fc776 100644
--- a/src/filesystem.rs
+++ b/src/filesystem.rs
@@ -12,7 +12,7 @@ use crate::database::entry::{Entry, EntryValue, InvariantEntry};
 use crate::database::hierarchies::{resolve_path_cached, ResolveCache, UNode, UPath};
 use crate::database::inner::models;
 use crate::database::{
-    file_set_valid, insert_entry, insert_file, retrieve_all_files, DbPool, DATABASE_FILENAME,
+    file_set_valid, insert_entry, insert_file, retrieve_all_files, DbPool, UPEND_SUBDIR,
 };
 use crate::util::hash::{Hash, Hashable};
 use crate::util::jobs::{Job, JobContainer, JobId, State};
@@ -80,6 +80,7 @@ pub async fn rescan_vault(
 
 type UpdatePathResult = Result<UpdatePathOutcome>;
 
+#[derive(Debug, Clone)]
 enum UpdatePathOutcome {
     Added(PathBuf),
     Unchanged(PathBuf),
@@ -105,17 +106,17 @@ fn _rescan_vault<T: AsRef<Path>>(
 
     // Walk through the vault, find all paths
     debug!("Traversing vault directory");
+    let absolute_dir_path = fs::canonicalize(&directory)?;
     let path_entries: Vec<PathBuf> = WalkDir::new(&directory)
         .follow_links(true)
         .into_iter()
         .filter_map(|e| e.ok())
-        .filter(|e| e.path().is_file() && e.file_name() != DATABASE_FILENAME)
         .map(|e| fs::canonicalize(e.into_path()).unwrap())
+        .filter(|e| !e.starts_with(&absolute_dir_path.join(UPEND_SUBDIR)))
         .collect();
 
     // Prepare for processing
     let rw_pool = Arc::new(RwLock::new(pool.clone()));
-    let absolute_path = fs::canonicalize(&directory)?;
     let existing_files = Arc::new(RwLock::new(retrieve_all_files(&pool.get()?)?));
 
     // Actual processing
@@ -129,7 +130,7 @@ fn _rescan_vault<T: AsRef<Path>>(
                 &rw_pool,
                 &resolve_cache,
                 path,
-                &absolute_path,
+                &absolute_dir_path,
                 &existing_files,
             )?;