Custom Field add markup to line breaks

I believe this is what you are after:

// define $post_id, $key, $single
$multipleLineValue = get_post_meta($post_id, $key, $single);

// Convert into an array where desired code can be added to the output
$multipleLineValue = explode("\n",$multipleLineValue);
$output = "";
foreach ($multipleLineValue as $lineValue) {
   $output .= "<span>".$lineValue."</span><br>";
}
echo $output;