diff --git a/bin/pyenv-sh-deactivate b/bin/pyenv-sh-deactivate
index c49d1cf..524aa5e 100755
--- a/bin/pyenv-sh-deactivate
+++ b/bin/pyenv-sh-deactivate
@@ -28,9 +28,9 @@ while [ $# -gt 0 ]; do
 done
 
 shell="$(basename "${PYENV_SHELL:-$SHELL}")"
-prefix="${PYENV_ACTIVATE:-${VIRTUAL_ENV}}"
+prefix="${VIRTUAL_ENV:-${PYENV_ACTIVATE}}"
 
-if [ -z "${VIRTUAL_ENV}" ]; then
+if [ -z "${prefix}" ]; then
   [ -n "$QUIET" ] || echo "pyenv-virtualenv: no virtualenv has been activated." 1>&2
   echo "false"
   exit 1
diff --git a/bin/pyenv-virtualenv-init b/bin/pyenv-virtualenv-init
index bfd03ff..50d501c 100755
--- a/bin/pyenv-virtualenv-init
+++ b/bin/pyenv-virtualenv-init
@@ -102,24 +102,14 @@ case "$shell" in
 fish )
   cat <<EOS
 function _pyenv_virtualenv_hook --on-event fish_prompt;
-  set -l PYENV_PREFIX (pyenv prefix 2>/dev/null; or true)
   set -l ret \$status
-  if [ -n "\$PYENV_ACTIVATE" ]
-    if [ (pyenv version-name 2>/dev/null; or true) = "system" ]
-      pyenv deactivate --quiet
-      set -e PYENV_DEACTIVATE
-      return \$ret
-    end
-    if [ "\$PYENV_ACTIVATE" != "\$PYENV_PREFIX" ]
-      if pyenv deactivate --quiet
-        set -e PYENV_DEACTIVATE
-        pyenv activate --quiet; or set -e PYENV_DEACTIVATE
-      else
-        pyenv activate --quiet
-      end
+  if [ -n "\$VIRTUAL_ENV" ]
+    if [ "\$VIRTUAL_ENV" != (pyenv prefix 2>/dev/null; or true) ]
+      pyenv deactivate --quiet; or true
+      pyenv activate --quiet; or true
     end
   else
-    if [ -z "\$VIRTUAL_ENV" ]; and [ "\$PYENV_DEACTIVATE" != "\$PYENV_PREFIX" ]
+    if [ "\$PYENV_DEACTIVATE" != (pyenv prefix 2>/dev/null; or true) ]
       pyenv activate --quiet; or true
     end
   end
@@ -142,22 +132,13 @@ esac
 if [[ "$shell" != "fish" ]]; then
   cat <<EOS
   local ret=\$?
-  if [ -n "\$PYENV_ACTIVATE" ]; then
-    if [ "\$(pyenv version-name 2>/dev/null || true)" = "system" ]; then
-      eval "\$(pyenv sh-deactivate --quiet)"
-      unset PYENV_DEACTIVATE
-      return \$ret
-    fi
-    if [ "\$PYENV_ACTIVATE" != "\$(pyenv prefix 2>/dev/null || true)" ]; then
-      if eval "\$(pyenv sh-deactivate --quiet)"; then
-        unset PYENV_DEACTIVATE
-        eval "\$(pyenv sh-activate --quiet)" || unset PYENV_DEACTIVATE
-      else
-        eval "\$(pyenv sh-activate --quiet)"
-      fi
+  if [ -n "\$VIRTUAL_ENV" ]; then
+    if [ "\$VIRTUAL_ENV" != "\$(pyenv prefix 2>/dev/null || true)" ]; then
+      eval "\$(pyenv sh-deactivate --quiet)" || true
+      eval "\$(pyenv sh-activate --quiet)" || true
     fi
   else
-    if [ -z "\$VIRTUAL_ENV" ] && [ "\$PYENV_DEACTIVATE" != "\$(pyenv prefix 2>/dev/null || true)" ]; then
+    if [ "\$PYENV_DEACTIVATE" != "\$(pyenv prefix 2>/dev/null || true)" ]; then
       eval "\$(pyenv sh-activate --quiet)" || true
     fi
   fi