diff --git a/src/config_file.c b/src/config_file.c
index 56271144b..393a0b547 100644
--- a/src/config_file.c
+++ b/src/config_file.c
@@ -1522,6 +1522,9 @@ static int config_write(diskfile_backend *cfg, const char *key, const regex_t *p
 
 			git_filebuf_write(&file, reader->buffer.ptr, reader->buffer.size);
 
+			if (reader->buffer.size > 0 && *(reader->buffer.ptr + reader->buffer.size - 1) != '\n')
+				git_filebuf_write(&file, "\n", 1);
+
 			/* And now if we just need to add a variable */
 			if (!section_matches && write_section(&file, section) < 0)
 				goto rewrite_fail;
@@ -1536,9 +1539,6 @@ static int config_write(diskfile_backend *cfg, const char *key, const regex_t *p
 			}
 
 			/* If we are here, there is at least a section line */
-			if (reader->buffer.size > 0 && *(reader->buffer.ptr + reader->buffer.size - 1) != '\n')
-				git_filebuf_write(&file, "\n", 1);
-
 			q = quotes_for_value(value);
 			git_filebuf_printf(&file, "\t%s = %s%s%s\n", name, q, value, q);
 		}