How to modify the subfields of a custom field in hook presave
As @sonfd commented you could get the field content as array:
$values = $entity-&gt;get('field_multifield')-&gt;getValue();

modify this array
$values[0]['prefix'] = '55555';

and then replace the entire field content:
$entity-&gt;set('field_multifield', $values);

Much easier though would be accessing a single property directly:
$entity-&gt;field_multifield-&gt;prefix = '55555';