How can I update a custom Order field in a plugin controller?
Turns out I really overthought this one! It's exactly the same as you would usually do it in Craft.

$this-&gt;cart-&gt;getContent()-&gt;setAttributes(array(
    'orderShippingOptions' =&gt; $myValue
));

craft()-&gt;commerce_orders-&gt;saveOrder($this-&gt;cart);


The bit I was missing was craft()-&gt;commerce_orders-&gt;saveOrder($this-&gt;cart);