diff --git a/include/builders/external_memory_builder_partitioned_phf.hpp b/include/builders/external_memory_builder_partitioned_phf.hpp
index f56c319..ae2a5c0 100644
--- a/include/builders/external_memory_builder_partitioned_phf.hpp
+++ b/include/builders/external_memory_builder_partitioned_phf.hpp
@@ -281,7 +281,11 @@ struct external_memory_builder_partitioned_phf {
 
     struct meta_partition {
         meta_partition(std::string const& dir_name, uint64_t id)
-            : m_filename(dir_name + "/pthash.temp." + std::to_string(id)), m_size(0) {}
+            : m_filename(dir_name + "/pthash.temp." + std::to_string(id)), m_size(0) {
+            // Truncate the file if it exists from a previous run
+            std::ofstream truncate(m_filename.c_str(), std::ofstream::binary | std::ofstream::trunc);
+            truncate.close();
+        }
 
         void push_back(hash_type hash) {
             m_hashes.push_back(hash);
@@ -322,4 +326,4 @@ struct external_memory_builder_partitioned_phf {
     };
 };
 
-}  // namespace pthash
\ No newline at end of file
+}  // namespace pthash