diff --git a/include/silo/preprocessing/metadata_info.h b/include/silo/preprocessing/metadata_info.h
index 6457def10..d85c51090 100644
--- a/include/silo/preprocessing/metadata_info.h
+++ b/include/silo/preprocessing/metadata_info.h
@@ -15,6 +15,7 @@ class MetadataInfo {
       const silo::config::DatabaseConfig& database_config
    );
 
+   static bool isNdjsonFileEmpty(const std::filesystem::path& ndjson_file);
    static void validateNdjsonFile(
       const std::filesystem::path& ndjson_file,
       const silo::config::DatabaseConfig& database_config
diff --git a/src/silo/preprocessing/metadata_info.cpp b/src/silo/preprocessing/metadata_info.cpp
index dd3c59db1..e2993ac43 100644
--- a/src/silo/preprocessing/metadata_info.cpp
+++ b/src/silo/preprocessing/metadata_info.cpp
@@ -85,6 +85,21 @@ void MetadataInfo::validateMetadataFile(
    }
 }
 
+bool MetadataInfo::isNdjsonFileEmpty(const std::filesystem::path& ndjson_file) {
+   duckdb::DuckDB duck_db(nullptr);
+   duckdb::Connection connection(duck_db);
+
+   auto result = connection.Query(fmt::format(
+      "SELECT COUNT(*) "
+      "FROM read_json_auto(\"{}\");",
+      ndjson_file.string()
+   ));
+
+   auto row_count_value = result->GetValue<int64_t>(0, 0);
+   const int64_t row_count = duckdb::BigIntValue::Get(row_count_value);
+   return row_count == 0;
+}
+
 void MetadataInfo::validateNdjsonFile(
    const std::filesystem::path& ndjson_file,
    const silo::config::DatabaseConfig& database_config
diff --git a/src/silo/preprocessing/preprocessor.cpp b/src/silo/preprocessing/preprocessor.cpp
index cc9aca88b..953286ce1 100644
--- a/src/silo/preprocessing/preprocessor.cpp
+++ b/src/silo/preprocessing/preprocessor.cpp
@@ -134,7 +134,7 @@ void Preprocessor::buildTablesFromNdjsonInput(const std::filesystem::path& file_
       );
    }
 
-   if (std::filesystem::is_empty(file_name)) {
+   if (MetadataInfo::isNdjsonFileEmpty(file_name)) {
       SPDLOG_WARN(
          "The specified input file {} is empty. Ignoring its content.", file_name.string()
       );
@@ -325,7 +325,7 @@ void Preprocessor::createPartitionedSequenceTablesFromNdjson(const std::filesyst
 
 void Preprocessor::createAlignedPartitionedSequenceViews(const std::filesystem::path& file_name) {
    std::string file_reader_sql;
-   if (std::filesystem::is_empty(file_name)) {
+   if (MetadataInfo::isNdjsonFileEmpty(file_name)) {
       file_reader_sql = fmt::format(
          "SELECT ''::VARCHAR AS key, 'NULL'::VARCHAR AS partition_key {} {} {} {} {} LIMIT 0",
          boost::join(silo::prepend(", ''::VARCHAR AS ", prefixed_nuc_sequences), ""),
@@ -419,7 +419,7 @@ void Preprocessor::createAlignedPartitionedSequenceViews(const std::filesystem::
 void Preprocessor::createUnalignedPartitionedSequenceFiles(const std::filesystem::path& file_name) {
    for (const auto& [seq_name, _] : reference_genomes_.raw_nucleotide_sequences) {
       const std::string file_reader_sql =
-         std::filesystem::is_empty(file_name)
+         MetadataInfo::isNdjsonFileEmpty(file_name)
             ? fmt::format(
                  "SELECT ''::VARCHAR AS key, 'NULL'::VARCHAR as partition_key,"
                  " ''::VARCHAR AS unaligned_nuc_{} LIMIT 0",
diff --git a/src/silo/preprocessing/sequence_info.cpp b/src/silo/preprocessing/sequence_info.cpp
index 42397aba1..a4e6f93cf 100644
--- a/src/silo/preprocessing/sequence_info.cpp
+++ b/src/silo/preprocessing/sequence_info.cpp
@@ -2,6 +2,7 @@
 
 #include <duckdb.hpp>
 
+#include "silo/preprocessing/metadata_info.h"
 #include "silo/preprocessing/preprocessing_database.h"
 #include "silo/preprocessing/preprocessing_exception.h"
 #include "silo/preprocessing/sql_function.h"
@@ -106,7 +107,7 @@ void SequenceInfo::validateNdjsonFile(
    duckdb::Connection& connection,
    const std::filesystem::path& input_filename
 ) {
-   if (std::filesystem::is_empty(input_filename)) {
+   if (MetadataInfo::isNdjsonFileEmpty(input_filename)) {
       return;
    }
 
diff --git a/testBaseData/emptyInputNdjson/input_file.ndjson b/testBaseData/emptyInputNdjson/input_file.ndjson
index e69de29bb..8b1378917 100644
--- a/testBaseData/emptyInputNdjson/input_file.ndjson
+++ b/testBaseData/emptyInputNdjson/input_file.ndjson
@@ -0,0 +1 @@
+