Soft delete on a intermediate table for many-to-many relationship

You can put a constraint on the Eager Load:

public function groups()
    {

        return $this
        ->belongsToMany('Group')
        ->whereNull('group_user.deleted_at') // Table `group_user` has column `deleted_at`
        ->withTimestamps(); // Table `group_user` has columns: `created_at`, `updated_at`

    }

Instead of HARD deleting the relationship using:

User::find(1)->groups()->detach();

You should use something like this to SOFT delete instead:

DB::table('group_user')
    ->where('user_id', $user_id)
    ->where('group_id', $group_id)
    ->update(array('deleted_at' => DB::raw('NOW()')));