You'll need to do something with the_terms
which is the WordPress function for pulling out taxonomy data.
Something similar to below:
<?php query_posts( array( 'meta_key' => 'ratings_average', 'orderby' => 'meta_value_num', 'order' => 'DESC', 'post_type' => 'muffins', 'showposts' => 1) );
while ( have_posts() ) : the_post(); ?>
<div class="recipe">
<?php the_post_thumbnail(array(272,150)); ?>
<a href="<?php the_permalink(); ?>" alt="<?php the_title(); ?>"><p class="title"><?php the_title(); ?></p>
<p class="recipe-contents"><?php the_excerpt(); ?></p></a>
<ul>
<li>Preparation time: <?php the_terms( get_the_ID(), 'time'); ?> </li>
<li>Difficulty: <?php the_terms( get_the_ID(), 'difficulty'); ?></li>
<li>Servings: <?php the_terms( get_the_ID(), 'servings'); ?></li>
</ul>
<?php endwhile;?>
You can read more about the_terms()
here and how you can better use it with more styling, separators etc.
Hopefully this should answer your question.