diff --git a/pkgs/stdenv/generic/setup.sh b/pkgs/stdenv/generic/setup.sh
index c478c3753233..feb82fd92266 100644
--- a/pkgs/stdenv/generic/setup.sh
+++ b/pkgs/stdenv/generic/setup.sh
@@ -376,7 +376,8 @@ export NIX_BUILD_CORES
 
 # Prevent OpenSSL-based applications from using certificates in
 # /etc/ssl.
-if [ -z "$SSL_CERT_FILE" ]; then
+# Leave it in shells for convenience.
+if [ -z "$SSL_CERT_FILE" ] && [ -z "$IN_NIX_SHELL" ]; then
   export SSL_CERT_FILE=/no-cert-file.crt
 fi