diff --git a/app/main.go b/app/main.go
deleted file mode 100644
index e69de29..0000000
diff --git a/cmd/main.go b/cmd/main.go
new file mode 100644
index 0000000..33b8a1c
--- /dev/null
+++ b/cmd/main.go
@@ -0,0 +1,28 @@
+package main
+
+import (
+	"database/sql"
+	"log"
+	"path/filepath"
+
+	migrate "github.com/KristianJBorgwarth/dendrite.daemon/persistence"
+	_ "modernc.org/sqlite"
+)
+
+func main() {
+	dbPath := filepath.Join("persistence", "index.db")
+
+	db, err := sql.Open("sqlite", dbPath)
+	if err != nil {
+		log.Fatal(err)
+	}
+	defer db.Close()
+
+	migrationsDir := filepath.Join("persistence", "migrations")
+
+	if err := migrate.Run(db, migrationsDir); err != nil {
+		log.Fatal(err)
+	}
+
+	log.Println("migrations applied successfully")
+}
diff --git a/go.mod b/go.mod
index 176ad5e..ceb31eb 100644
--- a/go.mod
+++ b/go.mod
@@ -2,3 +2,15 @@ module github.com/KristianJBorgwarth/dendrite.daemon
 
 go 1.26
 
+require (
+	github.com/dustin/go-humanize v1.0.1 // indirect
+	github.com/google/uuid v1.6.0 // indirect
+	github.com/mattn/go-isatty v0.0.20 // indirect
+	github.com/ncruces/go-strftime v1.0.0 // indirect
+	github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec // indirect
+	golang.org/x/sys v0.42.0 // indirect
+	modernc.org/libc v1.70.0 // indirect
+	modernc.org/mathutil v1.7.1 // indirect
+	modernc.org/memory v1.11.0 // indirect
+	modernc.org/sqlite v1.47.0 // indirect
+)
diff --git a/go.sum b/go.sum
index e69de29..988cc37 100644
--- a/go.sum
+++ b/go.sum
@@ -0,0 +1,21 @@
+github.com/dustin/go-humanize v1.0.1 h1:GzkhY7T5VNhEkwH0PVJgjz+fX1rhBrR7pRT3mDkpeCY=
+github.com/dustin/go-humanize v1.0.1/go.mod h1:Mu1zIs6XwVuF/gI1OepvI0qD18qycQx+mFykh5fBlto=
+github.com/google/uuid v1.6.0 h1:NIvaJDMOsjHA8n1jAhLSgzrAzy1Hgr+hNrb57e+94F0=
+github.com/google/uuid v1.6.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
+github.com/mattn/go-isatty v0.0.20 h1:xfD0iDuEKnDkl03q4limB+vH+GxLEtL/jb4xVJSWWEY=
+github.com/mattn/go-isatty v0.0.20/go.mod h1:W+V8PltTTMOvKvAeJH7IuucS94S2C6jfK/D7dTCTo3Y=
+github.com/ncruces/go-strftime v1.0.0 h1:HMFp8mLCTPp341M/ZnA4qaf7ZlsbTc+miZjCLOFAw7w=
+github.com/ncruces/go-strftime v1.0.0/go.mod h1:Fwc5htZGVVkseilnfgOVb9mKy6w1naJmn9CehxcKcls=
+github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec h1:W09IVJc94icq4NjY3clb7Lk8O1qJ8BdBEF8z0ibU0rE=
+github.com/remyoudompheng/bigfft v0.0.0-20230129092748-24d4a6f8daec/go.mod h1:qqbHyh8v60DhA7CoWK5oRCqLrMHRGoxYCSS9EjAz6Eo=
+golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.42.0 h1:omrd2nAlyT5ESRdCLYdm3+fMfNFE/+Rf4bDIQImRJeo=
+golang.org/x/sys v0.42.0/go.mod h1:4GL1E5IUh+htKOUEOaiffhrAeqysfVGipDYzABqnCmw=
+modernc.org/libc v1.70.0 h1:U58NawXqXbgpZ/dcdS9kMshu08aiA6b7gusEusqzNkw=
+modernc.org/libc v1.70.0/go.mod h1:OVmxFGP1CI/Z4L3E0Q3Mf1PDE0BucwMkcXjjLntvHJo=
+modernc.org/mathutil v1.7.1 h1:GCZVGXdaN8gTqB1Mf/usp1Y/hSqgI2vAGGP4jZMCxOU=
+modernc.org/mathutil v1.7.1/go.mod h1:4p5IwJITfppl0G4sUEDtCr4DthTaT47/N3aT6MhfgJg=
+modernc.org/memory v1.11.0 h1:o4QC8aMQzmcwCK3t3Ux/ZHmwFPzE6hf2Y5LbkRs+hbI=
+modernc.org/memory v1.11.0/go.mod h1:/JP4VbVC+K5sU2wZi9bHoq2MAkCnrt2r98UGeSK7Mjw=
+modernc.org/sqlite v1.47.0 h1:R1XyaNpoW4Et9yly+I2EeX7pBza/w+pmYee/0HJDyKk=
+modernc.org/sqlite v1.47.0/go.mod h1:hWjRO6Tj/5Ik8ieqxQybiEOUXy0NJFNp2tpvVpKlvig=
diff --git a/persistence/db_migrator.go b/persistence/db_migrator.go
new file mode 100644
index 0000000..867d049
--- /dev/null
+++ b/persistence/db_migrator.go
@@ -0,0 +1,70 @@
+// Package migrate handles database schema migrations
+package migrate
+
+import (
+	"database/sql"
+	"os"
+	"path/filepath"
+	"sort"
+)
+
+func Run(db *sql.DB, dir string) error {
+	_, err := db.Exec(`CREATE TABLE IF NOT EXISTS schema_migrations (version TEXT PRIMARY KEY);`)
+	if err != nil {
+		return err
+	}
+
+	entries, err := os.ReadDir(dir)
+	if err != nil {
+		return err
+	}
+
+	sort.Slice(entries, func(i, j int) bool {
+		return entries[i].Name() < entries[j].Name()
+	})
+
+	for _, e := range entries {
+		if e.IsDir(){
+			continue
+		}
+
+		name := e.Name()
+
+		applied, err := isMigrationApplied(db, name)
+		if err != nil {
+			return err
+		}
+
+		if applied {
+			continue
+		}
+
+		path := filepath.Join(dir, name)
+
+		sqlBytes, err := os.ReadFile(path)
+		if err != nil {
+			return err
+		}
+
+		if _, err := db.Exec(string(sqlBytes)); err != nil {
+			return err
+		}
+
+		if _, err := db.Exec(`INSERT INTO schema_migrations (version) VALUES (?)`, name); err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+func isMigrationApplied(db *sql.DB, version string) (bool, error) {
+	var v string
+	err := db.QueryRow(`SELECT version FROM schema_migrations WHERE version= ?`, version).Scan(&v)
+
+	if err == sql.ErrNoRows {
+		return false, nil
+	}
+
+	return err == nil, err
+}
diff --git a/persistence/index.db b/persistence/index.db
new file mode 100644
index 0000000..d7c1874
Binary files /dev/null and b/persistence/index.db differ
diff --git a/persistence/index.go b/persistence/index.go
deleted file mode 100644
index e69de29..0000000
diff --git a/persistence/migrations/001_dendrite_db_init.sql b/persistence/migrations/001_dendrite_db_init.sql
new file mode 100644
index 0000000..1ebfc49
--- /dev/null
+++ b/persistence/migrations/001_dendrite_db_init.sql
@@ -0,0 +1,21 @@
+CREATE TABLE IF NOT EXISTS notes (
+    id INTEGER PRIMARY KEY,
+    path TEXT UNIQUE,
+    title TEXT,
+    slug TEXT UNIQUE NOT NULL,
+    created_at TEXT NOT NULL,
+    updated_at TEXT NOT NULL
+);
+
+CREATE TABLE IF NOT EXISTS links (
+    from_note_id INTEGER NOT NULL,
+    to_note_id INTEGER NOT NULL,
+    raw TEXT,
+    FOREIGN KEY(from_note_id) REFERENCES notes(id) ON DELETE CASCADE,
+    FOREIGN KEY(to_note_id) REFERENCES notes(id) ON DELETE CASCADE
+);
+
+CREATE INDEX IF NOT EXISTS idx_notes_slug ON notes(slug);
+CREATE INDEX IF NOT EXISTS idx_links_from ON links(from_note_id);
+CREATE INDEX IF NOT EXISTS idx_links_to ON links(to_note_id);
+
diff --git a/persistence/migrations/002_tags.sql b/persistence/migrations/002_tags.sql
new file mode 100644
index 0000000..739968a
--- /dev/null
+++ b/persistence/migrations/002_tags.sql
@@ -0,0 +1,12 @@
+CREATE TABLE IF NOT EXISTS tags (
+  id INTEGER PRIMARY KEY,
+  name TEXT UNIQUE
+);
+
+CREATE TABLE IF NOT EXISTS note_tags (
+  note_id INTEGER,
+  tag_id INTEGER,
+  PRIMARY KEY (note_id, tag_id),
+  FOREIGN KEY(note_id) REFERENCES notes(id) ON DELETE CASCADE,
+  FOREIGN KEY(tag_id) REFERENCES tags(id) ON DELETE CASCADE
+);
diff --git a/persistence/repository/note_repository.go b/persistence/repository/note_repository.go
deleted file mode 100644
index e69de29..0000000