Drupal - Programmatically update an entity reference field

You need to use code similar to the following.

    $node = Node::load($nid);     
    $node->field_code_used_by->target_id = $user_id;
    $node->save();

For a multiple-value field, to add the value to the end of the list, use the following code.

$node->field_code_used_by[] = ['target_id' => $user_id];

Another way is setting the entity property with the entity object, as in the following code.

    $node = Node::load($nid);
    $user = \Drupal\user\Entity\User::load(1);
    $node->field_code_used_by->entity = $user;
    $node->save();

Like in D7 the main property of a reference field in D8 is still the target id:

$node->field_code_used_by->target_id = $user_id;

The entity property is a computed value. If you put an object in this value, drupal will convert it back to the id before saving it to the dababase.

Multivalue fields

Add an item to a multivalue field:

$node->field_code_used_by[] = ['target_id' => $user_id];

The property target_id is not necessary, because it is the main property and used by default. So for most fields you can add a value like in a simple php array, which is easy to remember:

$node->field_code_used_by[] = $user_id;

You should be aware of the difference between a single value field and a multiple value field. Code below shows how. Source: https://stefvanlooveren.me/blog/how-programmatically-update-entity-reference-field-drupal-8

$imageIds = [
  '3',
  '32',
  '50'
];
foreach($imageIds as $index => $fid) {
  if($index == 0) {
    $node->set('field_article_images', $fid);
  } else {
    $node->get('field_article_images')->appendItem([
      'target_id' => $fid,
    ]);
  }
}