diff -ru a/src/node_crypto.cc b/src/node_crypto.cc
--- a/src/node_crypto.cc	2017-03-31 22:39:56.483283868 +0200
+++ b/src/node_crypto.cc	2017-03-31 22:45:36.250267750 +0200
@@ -851,8 +851,6 @@
     }
   }
 
-  // Increment reference count so global store is not deleted along with CTX.
-  X509_STORE_up_ref(root_cert_store);
   SSL_CTX_set_cert_store(sc->ctx_, root_cert_store);
 }
 
diff -ru a/src/node_crypto.h b/src/node_crypto.h
--- a/src/node_crypto.h	2017-03-21 20:43:33.000000000 +0100
+++ b/src/node_crypto.h	2017-03-31 22:43:15.548183432 +0200
@@ -145,6 +145,13 @@
     }
 
     env()->isolate()->AdjustAmountOfExternalAllocatedMemory(-kExternalSize);
+    if (ctx_->cert_store == root_cert_store) {
+      // SSL_CTX_free() will attempt to free the cert_store as well.
+      // Since we want our root_cert_store to stay around forever
+      // we just clear the field. Hopefully OpenSSL will not modify this
+      // struct in future versions.
+      ctx_->cert_store = nullptr;
+    }
     SSL_CTX_free(ctx_);
     if (cert_ != nullptr)
       X509_free(cert_);