How can I put a custom field as the link of a button shortcode?

I think the problem is not with shortcode but with your code – you can’t nest blocks 😉

This should work just fine, I guess:

<?php echo do_shortcode("[standout-css3-button href="". get_post_meta($post->ID, "church-website-url', true) ."']Church website[/standout-css3-button]"); ?>

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