diff --git a/internal/importer/importer.go b/internal/importer/importer.go
index 262bf62c..14ed14b1 100644
--- a/internal/importer/importer.go
+++ b/internal/importer/importer.go
@@ -477,6 +477,7 @@ func upsertIssues(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, issues
 	// Track what we need to create
 	var newIssues []*types.Issue
 	seenHashes := make(map[string]bool)
+	seenIDs := make(map[string]bool) // Track IDs to prevent UNIQUE constraint errors
 
 	for _, incoming := range issues {
 		hash := incoming.ContentHash
@@ -486,13 +487,21 @@ func upsertIssues(ctx context.Context, sqliteStore *sqlite.SQLiteStorage, issues
 			incoming.ContentHash = hash
 		}
 
-		// Skip duplicates within incoming batch
+		// Skip duplicates within incoming batch (by content hash)
 		if seenHashes[hash] {
 			result.Skipped++
 			continue
 		}
 		seenHashes[hash] = true
 
+		// Skip duplicates by ID to prevent UNIQUE constraint violations
+		// This handles JSONL files with multiple versions of the same issue
+		if seenIDs[incoming.ID] {
+			result.Skipped++
+			continue
+		}
+		seenIDs[incoming.ID] = true
+
 		// CRITICAL: Check for tombstone FIRST, before any other matching (bd-4q8 fix)
 		// This prevents ghost resurrection regardless of which phase would normally match.
 		// If this ID has a tombstone in the DB, skip importing it entirely.
@@ -701,6 +710,20 @@ if len(newIssues) > 0 {
   return newIssues[i].ID < newIssues[j].ID // Stable sort
 })
 
+// Deduplicate by ID to prevent UNIQUE constraint errors during batch insert
+// This handles cases where JSONL contains multiple versions of the same issue
+seenNewIDs := make(map[string]bool)
+var dedupedNewIssues []*types.Issue
+for _, issue := range newIssues {
+	if !seenNewIDs[issue.ID] {
+		seenNewIDs[issue.ID] = true
+		dedupedNewIssues = append(dedupedNewIssues, issue)
+	} else {
+		result.Skipped++ // Count duplicates that were skipped
+	}
+}
+newIssues = dedupedNewIssues
+
 // Create in batches by depth level (max depth 3)
 		for depth := 0; depth <= 3; depth++ {
     var batchForDepth []*types.Issue
diff --git a/internal/storage/sqlite/issues.go b/internal/storage/sqlite/issues.go
index 91c17b57..23ec183a 100644
--- a/internal/storage/sqlite/issues.go
+++ b/internal/storage/sqlite/issues.go
@@ -4,10 +4,22 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
+	"strings"
 
 	"github.com/steveyegge/beads/internal/types"
 )
 
+// isUniqueConstraintError checks if error is a UNIQUE constraint violation
+// Used to detect and handle duplicate IDs in JSONL imports gracefully
+func isUniqueConstraintError(err error) bool {
+	if err == nil {
+		return false
+	}
+	errMsg := err.Error()
+	return strings.Contains(errMsg, "UNIQUE constraint failed") ||
+		strings.Contains(errMsg, "constraint failed: UNIQUE")
+}
+
 // insertIssue inserts a single issue into the database
 func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error {
 	sourceRepo := issue.SourceRepo
@@ -21,7 +33,7 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 	}
 
 	_, err := conn.ExecContext(ctx, `
-		INSERT INTO issues (
+		INSERT OR IGNORE INTO issues (
 			id, content_hash, title, description, design, acceptance_criteria, notes,
 			status, priority, issue_type, assignee, estimated_minutes,
 			created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
@@ -38,7 +50,12 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 		issue.Sender, ephemeral,
 	)
 	if err != nil {
-		return fmt.Errorf("failed to insert issue: %w", err)
+		// INSERT OR IGNORE should handle duplicates, but driver may still return error
+		// Explicitly ignore UNIQUE constraint errors (expected for duplicate IDs in JSONL)
+		if !isUniqueConstraintError(err) {
+			return fmt.Errorf("failed to insert issue: %w", err)
+		}
+		// Duplicate ID detected and ignored (INSERT OR IGNORE succeeded)
 	}
 	return nil
 }
@@ -46,7 +63,7 @@ func insertIssue(ctx context.Context, conn *sql.Conn, issue *types.Issue) error
 // insertIssues bulk inserts multiple issues using a prepared statement
 func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) error {
 	stmt, err := conn.PrepareContext(ctx, `
-		INSERT INTO issues (
+		INSERT OR IGNORE INTO issues (
 			id, content_hash, title, description, design, acceptance_criteria, notes,
 			status, priority, issue_type, assignee, estimated_minutes,
 			created_at, updated_at, closed_at, external_ref, source_repo, close_reason,
@@ -80,7 +97,12 @@ func insertIssues(ctx context.Context, conn *sql.Conn, issues []*types.Issue) er
 			issue.Sender, ephemeral,
 		)
 		if err != nil {
-			return fmt.Errorf("failed to insert issue %s: %w", issue.ID, err)
+			// INSERT OR IGNORE should handle duplicates, but driver may still return error
+			// Explicitly ignore UNIQUE constraint errors (expected for duplicate IDs in JSONL)
+			if !isUniqueConstraintError(err) {
+				return fmt.Errorf("failed to insert issue %s: %w", issue.ID, err)
+			}
+			// Duplicate ID detected and ignored (INSERT OR IGNORE succeeded)
 		}
 	}
 	return nil