diff --git a/TODO.md b/TODO.md
index 33cafc9..d3915ca 100644
--- a/TODO.md
+++ b/TODO.md
@@ -28,6 +28,11 @@ The other open issue is https://git.eeqj.de/sneak/routewatch/issues/30.
 
 # Completed Steps
 
+- 2026-10-03: a new database is created with `auto_vacuum` set to
+  incremental, through the connection string so it is set before the file
+  is first written, and each periodic incremental vacuum now returns up to
+  1000 free pages; the late `PRAGMA auto_vacuum` in `Initialize`, which
+  SQLite ignored, is gone (closes #43)
 - 2026-10-03: looking up an IP address no longer reads every IPv6 route:
   both families find the most specific live route with at most 33 or 129
   lookups on the prefix index, and the IPv4 range columns are gone. Prefixes
diff --git a/internal/database/database.go b/internal/database/database.go
index 14da155..6dfddbf 100644
--- a/internal/database/database.go
+++ b/internal/database/database.go
@@ -91,8 +91,13 @@ func New(cfg *config.Config, logger *logger.Logger) (*Database, error) {
 	// a transaction that reads before writing starts as a reader and, when it
 	// then writes while another connection holds the write lock, fails at once
 	// with "database is locked" without waiting for _busy_timeout.
+	// _auto_vacuum=incremental lets Vacuum return free pages to the filesystem.
+	// SQLite only accepts it before the database file is first written, and the
+	// switch to WAL writes it, so it must be here: the driver applies it on open,
+	// before _journal_mode. On an existing file it changes nothing.
 	dsn := fmt.Sprintf(
-		"file:%s?_cache_size=%d&_synchronous=OFF&_busy_timeout=%d&_journal_mode=WAL&_txlock=immediate",
+		"file:%s?_cache_size=%d&_synchronous=OFF&_busy_timeout=%d"+
+			"&_auto_vacuum=incremental&_journal_mode=WAL&_txlock=immediate",
 		dbPath,
 		sqliteCacheSizeKiB,
 		sqliteBusyTimeoutMs,
@@ -137,9 +142,8 @@ func (d *Database) Initialize() error {
 	// heap. The heap limits below are process-wide, so setting them once here is
 	// enough for the whole pool.
 	pragmas := []string{
-		"PRAGMA journal_mode=WAL",        // Write-Ahead Logging
-		"PRAGMA analysis_limit=0",        // Disable automatic ANALYZE
-		"PRAGMA auto_vacuum=INCREMENTAL", // Enable incremental vacuum
+		"PRAGMA journal_mode=WAL", // Write-Ahead Logging
+		"PRAGMA analysis_limit=0", // Disable automatic ANALYZE
 		fmt.Sprintf("PRAGMA soft_heap_limit=%d", sqliteSoftHeapLimitBytes),
 		fmt.Sprintf("PRAGMA hard_heap_limit=%d", sqliteHardHeapLimitBytes),
 	}
@@ -1857,10 +1861,20 @@ func (d *Database) Vacuum(ctx context.Context) error {
 	// Free up to 1000 pages per call (~4MB with default 4KB page size)
 	// This keeps each vacuum operation quick and non-blocking
 	const pagesToFree = 1000
-	_, err := d.db.ExecContext(ctx, fmt.Sprintf("PRAGMA incremental_vacuum(%d)", pagesToFree))
+	rows, err := d.db.QueryContext(ctx, fmt.Sprintf("PRAGMA incremental_vacuum(%d)", pagesToFree))
 	if err != nil {
 		return fmt.Errorf("failed to run incremental vacuum: %w", err)
 	}
+	defer func() { _ = rows.Close() }()
+
+	// SQLite frees one page each time the statement steps, and each step
+	// returns a row, so every row must be read for the pragma to free more
+	// than one page.
+	for rows.Next() {
+	}
+	if err := rows.Err(); err != nil {
+		return fmt.Errorf("failed to run incremental vacuum: %w", err)
+	}
 
 	return nil
 }
diff --git a/internal/database/database_test.go b/internal/database/database_test.go
index e15ec1a..82753a9 100644
--- a/internal/database/database_test.go
+++ b/internal/database/database_test.go
@@ -4,6 +4,7 @@ import (
 	"context"
 	"database/sql"
 	"errors"
+	"fmt"
 	"net/netip"
 	"sync"
 	"testing"
@@ -18,6 +19,13 @@ import (
 // memory"; the DSN change must leave temp_store below this so they spill to disk.
 const tempStoreMemory = 2
 
+// autoVacuumIncremental is the PRAGMA auto_vacuum value meaning "incremental".
+const autoVacuumIncremental = 2
+
+// vacuumTestRoutes is how many routes the vacuum test writes and then deletes,
+// enough to leave many free pages in the file.
+const vacuumTestRoutes = 2000
+
 // heldConnections is how many pooled connections the pragma test holds open at
 // once so each is a distinct SQLite connection that parsed the DSN.
 const heldConnections = 5
@@ -127,7 +135,8 @@ func TestGetIPInfoFindsMostSpecificLiveRoute(t *testing.T) {
 
 // TestConnectionPoolPragmas holds several pooled connections open at once and
 // checks each one carries the per-connection settings from the DSN, plus the
-// process-wide hard heap limit.
+// process-wide hard heap limit, and sees the new file with auto_vacuum
+// incremental.
 func TestConnectionPoolPragmas(t *testing.T) {
 	cfg := &config.Config{StateDir: t.TempDir()}
 
@@ -188,6 +197,74 @@ func TestConnectionPoolPragmas(t *testing.T) {
 		if hardHeapLimit != sqliteHardHeapLimitBytes {
 			t.Errorf("conn %d: hard_heap_limit = %d, want %d", i, hardHeapLimit, sqliteHardHeapLimitBytes)
 		}
+
+		var autoVacuum int
+		if err := c.QueryRowContext(ctx, "PRAGMA auto_vacuum").Scan(&autoVacuum); err != nil {
+			t.Fatalf("conn %d: failed to read auto_vacuum: %v", i, err)
+		}
+		if autoVacuum != autoVacuumIncremental {
+			t.Errorf("conn %d: auto_vacuum = %d, want %d (incremental)", i, autoVacuum, autoVacuumIncremental)
+		}
+	}
+}
+
+// TestVacuumReturnsFreePages checks that after routes are deleted from a new
+// database, one Vacuum call returns every page they used. The deletes leave
+// fewer free pages than the 1000 Vacuum frees per call, so none may remain.
+// With auto_vacuum off (issue https://git.eeqj.de/sneak/routewatch/issues/43)
+// the free pages stayed in the file, and with the PRAGMA run by ExecContext
+// Vacuum freed only one page per call.
+func TestVacuumReturnsFreePages(t *testing.T) {
+	cfg := &config.Config{StateDir: t.TempDir()}
+
+	db, err := New(cfg, logger.New())
+	if err != nil {
+		t.Fatalf("failed to create database: %v", err)
+	}
+	defer func() { _ = db.Close() }()
+
+	ctx := context.Background()
+	ts := time.Now().UTC()
+	const asn = 64500
+
+	routes := make([]*LiveRoute, 0, vacuumTestRoutes)
+	deletions := make([]LiveRouteDeletion, 0, vacuumTestRoutes)
+	for i := range vacuumTestRoutes {
+		route := mkV4Route(t, fmt.Sprintf("10.%d.%d.0/24", i/256, i%256), asn, ts)
+		routes = append(routes, route)
+		deletions = append(deletions, LiveRouteDeletion{
+			Prefix:    route.Prefix,
+			OriginASN: asn,
+			PeerIP:    route.PeerIP,
+			IPVersion: ipVersionV4,
+		})
+	}
+
+	if err := db.UpsertLiveRouteBatch(routes); err != nil {
+		t.Fatalf("failed to write routes: %v", err)
+	}
+	if err := db.DeleteLiveRouteBatch(deletions); err != nil {
+		t.Fatalf("failed to delete routes: %v", err)
+	}
+
+	var before int
+	if err := db.db.QueryRowContext(ctx, "PRAGMA freelist_count").Scan(&before); err != nil {
+		t.Fatalf("failed to read freelist_count: %v", err)
+	}
+	if before == 0 {
+		t.Fatalf("no free pages after deleting %d routes", vacuumTestRoutes)
+	}
+
+	if err := db.Vacuum(ctx); err != nil {
+		t.Fatalf("Vacuum failed: %v", err)
+	}
+
+	var after int
+	if err := db.db.QueryRowContext(ctx, "PRAGMA freelist_count").Scan(&after); err != nil {
+		t.Fatalf("failed to read freelist_count: %v", err)
+	}
+	if after != 0 {
+		t.Errorf("free pages after Vacuum = %d of %d, want 0", after, before)
 	}
 }