diff --git a/build_tests/configure/configure_with_top_level_env.rb b/build_tests/configure/configure_with_top_level_env.rb
new file mode 100644
index 0000000..3afe4bd
--- /dev/null
+++ b/build_tests/configure/configure_with_top_level_env.rb
@@ -0,0 +1,5 @@
+configure do
+  check_c_compiler
+end
+env do |env|
+end
diff --git a/lib/rscons/application.rb b/lib/rscons/application.rb
index f6d0450..7de5c6a 100644
--- a/lib/rscons/application.rb
+++ b/lib/rscons/application.rb
@@ -207,15 +207,18 @@ module Rscons
     #
     # @return [void]
     def configure
-      co = ConfigureOp.new(@script)
-      begin
-        @script.configure(co)
-      rescue RsconsError => e
-        co.close(false)
-        raise e
+      unless @_configured
+        @_configured = true
+        co = ConfigureOp.new(@script)
+        begin
+          @script.configure(co)
+        rescue RsconsError => e
+          co.close(false)
+          raise e
+        end
+        Cache.instance["configuration_data"]["enabled_variants"] = @enabled_variants
+        co.close(true)
       end
-      Cache.instance["configuration_data"]["enabled_variants"] = @enabled_variants
-      co.close(true)
     end
 
     # Remove installed files.
diff --git a/spec/build_tests_spec.rb b/spec/build_tests_spec.rb
index df2c15a..2f40f96 100644
--- a/spec/build_tests_spec.rb
+++ b/spec/build_tests_spec.rb
@@ -1836,6 +1836,15 @@ EOF
       expect(result.status).to_not eq 0
     end
 
+    it "only runs the configure operation once" do
+      test_dir "configure"
+
+      result = run_rscons(args: %w[-f configure_with_top_level_env.rb configure])
+      expect(result.stderr).to eq ""
+      expect(result.status).to eq 0
+      expect(result.stdout).to_not match %r{Configuring project.*Configuring project}m
+    end
+
     it "automatically runs the configure task if the project is not yet configured in the given build directory" do
       test_dir "configure"