diff --git a/CMakeLists.txt b/CMakeLists.txt
index cd19835feb..c210f61213 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -16,7 +16,7 @@ include_directories(BEFORE "${CMAKE_CURRENT_BINARY_DIR}/src/mirall/")
 
 include(GNUInstallDirs)
 ## stupid, we should upstream this
-if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr")
+if("${CMAKE_INSTALL_PREFIX}" STREQUAL "/usr" AND NOT CMAKE_INSTALL_SYSCONFIGDIR)
     set(CMAKE_INSTALL_SYSCONFDIR "/etc")
 endif()