diff --git a/cpp/src/arrow/filesystem/s3fs.cc b/cpp/src/arrow/filesystem/s3fs.cc
index ac373a69e7cd6..eaf4b789739aa 100644
--- a/cpp/src/arrow/filesystem/s3fs.cc
+++ b/cpp/src/arrow/filesystem/s3fs.cc
@@ -3483,7 +3483,14 @@ Status EnsureS3Initialized() {
 }
 
 Status FinalizeS3() {
-  GetAwsInstance()->Finalize();
+  auto instance = GetAwsInstance();
+  // The AWS instance might already be destroyed in case FinalizeS3
+  // is called from an atexit handler (which is a bad idea anyway as the
+  // AWS SDK is not safe anymore to shutdown by this time). See GH-44071.
+  if (instance == nullptr) {
+    return Status::Invalid("FinalizeS3 called too late");
+  }
+  instance->Finalize();
   return Status::OK();
 }