diff --git a/internal/db/bundb/migrations/20250415111056_thread_all_statuses.go b/internal/db/bundb/migrations/20250415111056_thread_all_statuses.go
index bfa4dd84f..daf392ee6 100644
--- a/internal/db/bundb/migrations/20250415111056_thread_all_statuses.go
+++ b/internal/db/bundb/migrations/20250415111056_thread_all_statuses.go
@@ -26,7 +26,6 @@ import (
 	"strings"
 	"time"
 
-	"code.superseriousbusiness.org/gotosocial/internal/db"
 	newmodel "code.superseriousbusiness.org/gotosocial/internal/db/bundb/migrations/20250415111056_thread_all_statuses/new"
 	oldmodel "code.superseriousbusiness.org/gotosocial/internal/db/bundb/migrations/20250415111056_thread_all_statuses/old"
 	"code.superseriousbusiness.org/gotosocial/internal/db/bundb/migrations/20250415111056_thread_all_statuses/util"
@@ -62,44 +61,80 @@ func init() {
 			return gtserror.Newf("error adding statuses column thread_id_new: %w", err)
 		}
 
-		var sr statusRethreader
-		var updatedRowsTotal int64
-		var maxID string
-		var statuses []*oldmodel.Status
+		if err := doWALCheckpoint(ctx, db); err != nil {
+			return err
+		}
 
-		// Get a total count of all statuses before migration.
-		total, err := db.NewSelect().Table("statuses").Count(ctx)
+		// Get a total count of all
+		// statuses before migration.
+		totalStatuses, err := db.
+			NewSelect().
+			Table("statuses").
+			Count(ctx)
 		if err != nil {
 			return gtserror.Newf("error getting status table count: %w", err)
 		}
+		log.Warnf(ctx, "migrating %d statuses total, this may take a *long* time", totalStatuses)
 
-		// Start at largest
+		var sr statusRethreader
+		var updatedRowsTotal int64
+		var statuses []*oldmodel.Status
+
+		// Page starting at largest
 		// possible ULID value.
-		maxID = id.Highest
+		var maxID = id.Highest
 
-		log.Warnf(ctx, "migrating %d statuses, this may take a *long* time", total)
-		for {
-			start := time.Now()
+		// Open initial transaction.
+		tx, err := db.BeginTx(ctx, nil)
+		if err != nil {
+			return err
+		}
+
+		for i := 1; ; i++ {
 
 			// Reset slice.
 			clear(statuses)
 			statuses = statuses[:0]
 
+			start := time.Now()
+
 			// Select IDs of next
 			// batch, paging down.
-			if err := db.NewSelect().
+			if err := tx.NewSelect().
 				Model(&statuses).
 				Column("id").
+				Where("? IS NULL", bun.Ident("in_reply_to_id")).
 				Where("? < ?", bun.Ident("id"), maxID).
 				OrderExpr("? DESC", bun.Ident("id")).
-				Limit(250).
+				Limit(100).
 				Scan(ctx); err != nil && !errors.Is(err, sql.ErrNoRows) {
-				return gtserror.Newf("error selecting unthreaded statuses: %w", err)
+				return gtserror.Newf("error selecting top-level statuses: %w", err)
+			}
+
+			// Every 50 loops, flush wal and begin new
+			// transaction, to avoid silly wal sizes.
+			if i%50 == 0 {
+				if err := tx.Commit(); err != nil {
+					return err
+				}
+
+				if err := doWALCheckpoint(ctx, db); err != nil {
+					return err
+				}
+
+				tx, err = db.BeginTx(ctx, nil)
+				if err != nil {
+					return err
+				}
 			}
 
 			// No more statuses!
 			l := len(statuses)
 			if l == 0 {
+				if err := tx.Commit(); err != nil {
+					return err
+				}
+
 				log.Info(ctx, "done migrating statuses!")
 				break
 			}
@@ -107,52 +142,137 @@ func init() {
 			// Set next maxID value from statuses.
 			maxID = statuses[l-1].ID
 
-			// Rethread each selected status in a transaction.
+			// Rethread inside the transaction.
 			var updatedRowsThisBatch int64
-			if err := db.RunInTx(ctx, nil, func(ctx context.Context, tx bun.Tx) error {
-				for _, status := range statuses {
-					n, err := sr.rethreadStatus(ctx, tx, status)
-					if err != nil {
-						return gtserror.Newf("error rethreading status %s: %w", status.URI, err)
-					}
-					updatedRowsThisBatch += n
-					updatedRowsTotal += n
+			for _, status := range statuses {
+				n, err := sr.rethreadStatus(ctx, tx, status)
+				if err != nil {
+					return gtserror.Newf("error rethreading status %s: %w", status.URI, err)
 				}
-
-				return nil
-			}); err != nil {
-				return err
+				updatedRowsThisBatch += n
+				updatedRowsTotal += n
 			}
 
-			// Show current speed + percent migrated.
-			//
-			// Percent may end up wonky due to approximations
-			// and batching, so show a generic message at 100%.
+			// Show speed for this batch.
 			timeTaken := time.Since(start).Milliseconds()
 			msPerRow := float64(timeTaken) / float64(updatedRowsThisBatch)
 			rowsPerMs := float64(1) / float64(msPerRow)
 			rowsPerSecond := 1000 * rowsPerMs
-			percentDone := (float64(updatedRowsTotal) / float64(total)) * 100
-			if percentDone <= 100 {
-				log.Infof(
-					ctx,
-					"[updated %d total rows, now @ ~%.0f rows/s] done ~%.2f%% of statuses",
-					updatedRowsTotal, rowsPerSecond, percentDone,
-				)
-			} else {
-				log.Infof(
-					ctx,
-					"[updated %d total rows, now @ ~%.0f rows/s] almost done... ",
-					updatedRowsTotal, rowsPerSecond,
-				)
-			}
+
+			// Show percent migrated overall.
+			totalDone := (float64(updatedRowsTotal) / float64(totalStatuses)) * 100
+
+			log.Infof(
+				ctx,
+				"[~%.2f%% done; ~%.0f rows/s] paging top-level statuses",
+				totalDone, rowsPerSecond,
+			)
 		}
 
-		// Attempt to merge any sqlite write-ahead-log.
 		if err := doWALCheckpoint(ctx, db); err != nil {
 			return err
 		}
 
+		// Reset max ID.
+		maxID = id.Highest
+
+		// Create a temporary index on thread_id_new for stragglers.
+		log.Info(ctx, "creating temporary statuses thread_id_new index")
+		if _, err := db.NewCreateIndex().
+			Table("statuses").
+			Index("statuses_thread_id_new_idx").
+			Column("thread_id_new").
+			Exec(ctx); err != nil {
+			return gtserror.Newf("error creating new thread_id index: %w", err)
+		}
+
+		// Open a new transaction lads.
+		tx, err = db.BeginTx(ctx, nil)
+		if err != nil {
+			return err
+		}
+
+		for i := 1; ; i++ {
+
+			// Reset slice.
+			clear(statuses)
+			statuses = statuses[:0]
+
+			start := time.Now()
+
+			// Select IDs of stragglers for
+			// which we haven't set thread_id yet.
+			if err := tx.NewSelect().
+				Model(&statuses).
+				Column("id").
+				Where("? = ?", bun.Ident("thread_id_new"), id.Lowest).
+				Limit(500).
+				Scan(ctx); err != nil && !errors.Is(err, sql.ErrNoRows) {
+				return gtserror.Newf("error selecting unthreaded statuses: %w", err)
+			}
+
+			// Every 50 loops, flush wal and begin new
+			// transaction, to avoid silly wal sizes.
+			if i%50 == 0 {
+				if err := tx.Commit(); err != nil {
+					return err
+				}
+
+				if err := doWALCheckpoint(ctx, db); err != nil {
+					return err
+				}
+
+				tx, err = db.BeginTx(ctx, nil)
+				if err != nil {
+					return err
+				}
+			}
+
+			// No more statuses!
+			l := len(statuses)
+			if l == 0 {
+				if err := tx.Commit(); err != nil {
+					return err
+				}
+
+				log.Info(ctx, "done migrating statuses!")
+				break
+			}
+
+			// Rethread inside the transaction.
+			var updatedRowsThisBatch int64
+			for _, status := range statuses {
+				n, err := sr.rethreadStatus(ctx, tx, status)
+				if err != nil {
+					return gtserror.Newf("error rethreading status %s: %w", status.URI, err)
+				}
+				updatedRowsThisBatch += n
+				updatedRowsTotal += n
+			}
+
+			// Show speed for this batch.
+			timeTaken := time.Since(start).Milliseconds()
+			msPerRow := float64(timeTaken) / float64(updatedRowsThisBatch)
+			rowsPerMs := float64(1) / float64(msPerRow)
+			rowsPerSecond := 1000 * rowsPerMs
+
+			// Show percent migrated overall.
+			totalDone := (float64(updatedRowsTotal) / float64(totalStatuses)) * 100
+
+			log.Infof(
+				ctx,
+				"[~%.2f%% done; ~%.0f rows/s] cleaning up stragglers",
+				totalDone, rowsPerSecond,
+			)
+		}
+
+		log.Info(ctx, "dropping temporary thread_id_new index")
+		if _, err := db.NewDropIndex().
+			Index("statuses_thread_id_new_idx").
+			Exec(ctx); err != nil {
+			return gtserror.Newf("error dropping temporary thread_id_new index: %w", err)
+		}
+
 		log.Info(ctx, "dropping old thread_to_statuses table")
 		if _, err := db.NewDropTable().
 			Table("thread_to_statuses").
@@ -265,17 +385,33 @@ func (sr *statusRethreader) rethreadStatus(ctx context.Context, tx bun.Tx, statu
 
 	// Ensure the passed status
 	// has up-to-date information.
-	// This may have changed from
-	// the initial batch selection
-	// to the rethreadStatus() call.
+	upToDateValues := make(map[string]any, 3)
 	if err := tx.NewSelect().
-		Model(status).
-		Column("in_reply_to_id", "thread_id").
+		TableExpr("? AS ?", bun.Ident("statuses"), bun.Ident("status")).
+		Column("in_reply_to_id", "thread_id", "thread_id_new").
 		Where("? = ?", bun.Ident("id"), status.ID).
-		Scan(ctx); err != nil {
+		Scan(ctx, &upToDateValues); err != nil {
 		return 0, gtserror.Newf("error selecting status: %w", err)
 	}
 
+	// If we've just threaded this status by setting
+	// thread_id_new, then by definition anything we
+	// could find from the entire thread must now be
+	// threaded, so we can save some database calls
+	// by skipping iterating up + down from here.
+	if v, ok := upToDateValues["thread_id_new"]; ok && v.(string) != id.Lowest {
+		log.Debug(ctx, "skipping just rethreaded status")
+		return 0, nil
+	}
+
+	// Set up-to-date values on the status.
+	if inReplyToID, ok := upToDateValues["in_reply_to_id"]; ok && inReplyToID != nil {
+		status.InReplyToID = inReplyToID.(string)
+	}
+	if threadID, ok := upToDateValues["thread_id"]; ok && threadID != nil {
+		status.ThreadID = threadID.(string)
+	}
+
 	// status and thread ID cursor
 	// index values. these are used
 	// to keep track of newly loaded
@@ -328,6 +464,7 @@ func (sr *statusRethreader) rethreadStatus(ctx context.Context, tx bun.Tx, statu
 	// batch of statuses is already correctly
 	// threaded. Then we have nothing to do!
 	if sr.allThreaded && len(sr.threadIDs) == 1 {
+		log.Debug(ctx, "skipping just rethreaded thread")
 		return 0, nil
 	}
 
@@ -479,7 +616,7 @@ func (sr *statusRethreader) getParents(ctx context.Context, tx bun.Tx) error {
 			Model(&parent).
 			Column("id", "in_reply_to_id", "thread_id").
 			Where("? = ?", bun.Ident("id"), id).
-			Scan(ctx); err != nil && err != db.ErrNoEntries {
+			Scan(ctx); err != nil && err != sql.ErrNoRows {
 			return err
 		}
 
@@ -518,7 +655,7 @@ func (sr *statusRethreader) getChildren(ctx context.Context, tx bun.Tx, idx int)
 			Model(&sr.statuses).
 			Column("id", "thread_id").
 			Where("? = ?", bun.Ident("in_reply_to_id"), id).
-			Scan(ctx); err != nil && err != db.ErrNoEntries {
+			Scan(ctx); err != nil && err != sql.ErrNoRows {
 			return err
 		}
 
@@ -557,7 +694,7 @@ func (sr *statusRethreader) getStragglers(ctx context.Context, tx bun.Tx, idx in
 			bun.Ident("id"),
 			bun.In(sr.statusIDs),
 		).
-		Scan(ctx); err != nil && err != db.ErrNoEntries {
+		Scan(ctx); err != nil && err != sql.ErrNoRows {
 		return err
 	}