diff -u b/field_collection.module b/field_collection.module
--- b/field_collection.module
+++ b/field_collection.module
@@ -1910,10 +1910,6 @@
   $delta = 0;
   $field = isset($entity->$target) ? $entity->$target : array();
   foreach ($value as $v) {
-    if (empty($v)) {
-      // Avoid creation of empty field collections
-      continue;
-    }
     if (isset($field['und'][$delta]['entity'])) {
       $field_collection_item = $field['und'][$delta]['entity'];
     }
@@ -1929,7 +1925,6 @@
       $callback($source, $field_collection_item, $sub_target, $v);
     }
 
-
     $field['und'][$delta]['entity'] = $field_collection_item;
     $field['und'][$delta]['value'] = $field_collection_item->item_id;
 
@@ -1945,0 +1941,40 @@
+
+/**
+ * Implements hook_feeds_presave().
+ */
+function field_collection_feeds_presave($source, $entity) {
+  // Do not save any empty field collection items that may have been created
+  // during the mapping process. Since the mapping is done field by field in
+  // field_collection_feeds_set_target(), we have to wait until this hook (when
+  // the field collection item is fully built up) before we can check if it's
+  // empty.
+  $config = $source->importer()->getConfig();
+  if (!empty($config['processor']['config']['mappings'])) {
+    // Find all field collection mappings.
+    foreach ($config['processor']['config']['mappings'] as $mapping) {
+      if (isset($mapping['target'])) {
+        $args = explode(':', $mapping['target']);
+        $field_name = array_shift($args);
+        if (($field = field_info_field($field_name)) && $field['type'] == 'field_collection') {
+          // If the field collection item is empty, do not save it.
+          if (!empty($entity->{$field_name})) {
+            foreach ($entity->{$field_name} as $langcode => &$items) {
+              foreach ($items as $delta => $item) {
+                if (isset($item['entity']) && field_collection_item_is_empty($item['entity'])) {
+                  unset($items[$delta]);
+                }
+              }
+              // Clean up the final array.
+              if (empty($items)) {
+                unset($entity->{$field_name}[$langcode]);
+              }
+              else {
+                $items = array_values($items);
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+}