diff --git a/Makefile b/Makefile
index b2aa27b92..fd3a2add4 100755
--- a/Makefile
+++ b/Makefile
@@ -81,6 +81,8 @@ clean:
 	@find ./src/ -name "*.so" -exec rm {} \;
 	@find ./ -name "*.o" -exec rm {} \;
 	@find ./src/ -name "*.a" -exec rm {} \;
+	@find ./ -name "*.gcda" -exec rm {} \;
+	@find ./ -name "*.gcno" -exec rm {} \;
 
 distclean:
 	if test -e "config.py"; then mv "config.py" "config.py.backup"; fi
diff --git a/SConstruct b/SConstruct
index 2b851e42d..9bc152641 100644
--- a/SConstruct
+++ b/SConstruct
@@ -293,6 +293,7 @@ opts.AddVariables(
     EnumVariable('OPTIMIZATION','Set compiler optimization level','3', ['0','1','2','3','4','s']),
     # Note: setting DEBUG=True will override any custom OPTIMIZATION level
     BoolVariable('DEBUG', 'Compile a debug version of Mapnik', 'False'),
+    BoolVariable('COVERAGE', 'Compile a libmapnik and plugins with --coverage', 'False'),
     BoolVariable('DEBUG_UNDEFINED', 'Compile a version of Mapnik using clang/llvm undefined behavior asserts', 'False'),
     BoolVariable('DEBUG_SANITIZE', 'Compile a version of Mapnik using clang/llvm address sanitation', 'False'),
     ListVariable('INPUT_PLUGINS','Input drivers to include',DEFAULT_PLUGINS,PLUGINS.keys()),
@@ -1139,6 +1140,9 @@ if not preconfigured:
     else:
         mode = 'release mode'
 
+    if env['COVERAGE']:
+        mode += ' (with coverage)'
+
     env['PLATFORM'] = platform.uname()[0]
     color_print(4,"Configuring on %s in *%s*..." % (env['PLATFORM'],mode))
 
@@ -1891,6 +1895,10 @@ if not HELP_REQUESTED:
 
     plugin_base = env.Clone()
 
+    if env['COVERAGE']:
+        plugin_base.Append(LINKFLAGS='--coverage')
+        plugin_base.Append(CXXFLAGS='--coverage')
+
     Export('plugin_base')
 
     if env['FAST']:
diff --git a/scripts/travis-common.sh b/scripts/travis-common.sh
index cfdc57f59..edf90f619 100644
--- a/scripts/travis-common.sh
+++ b/scripts/travis-common.sh
@@ -82,8 +82,7 @@ config_override () {
 configure () {
     if enabled ${COVERAGE}; then
         ./configure "$@" PGSQL2SQLITE=False SVG2PNG=False SVG_RENDERER=False \
-            CUSTOM_LDFLAGS='--coverage' CUSTOM_CXXFLAGS='--coverage' \
-            CUSTOM_CFLAGS='--coverage' DEBUG=True
+            COVERAGE=True DEBUG=True
     elif enabled ${MASON_PUBLISH}; then
         export MASON_NAME=mapnik
         export MASON_VERSION=latest
@@ -101,9 +100,10 @@ configure () {
 
 coverage () {
     ./mason_packages/.link/bin/cpp-coveralls \
-        --build-root . --gcov-options '\-lp' --exclude mason_packages \
+        --build-root . --gcov-options '\-lp' \
+        --exclude mason_packages \
         --exclude .sconf_temp --exclude benchmark --exclude deps \
         --exclude scons --exclude test --exclude demo --exclude docs \
-        --exclude fonts --exclude utils \
+        --exclude fonts \
         > /dev/null
 }
diff --git a/src/build.py b/src/build.py
index 1568e9c34..c586cf130 100644
--- a/src/build.py
+++ b/src/build.py
@@ -62,6 +62,10 @@ system = 'boost_system%s' % env['BOOST_APPEND']
 lib_env['LIBS'] = [filesystem,
                    regex]
 
+if env['COVERAGE']:
+    lib_env.Append(LINKFLAGS='--coverage')
+    lib_env.Append(CXXFLAGS='--coverage')
+
 if env['HAS_CAIRO']:
     lib_env.Append(LIBS=env['CAIRO_ALL_LIBS'])
 
diff --git a/utils/mapnik-index/build.py b/utils/mapnik-index/build.py
index 651075ae7..358ce5f88 100644
--- a/utils/mapnik-index/build.py
+++ b/utils/mapnik-index/build.py
@@ -24,8 +24,9 @@ import glob
 from copy import copy
 
 Import ('env')
+Import ('plugin_base')
 
-program_env = env.Clone()
+program_env = plugin_base.Clone()
 
 source = Split(
     """
@@ -36,7 +37,6 @@ source = Split(
     """
     )
 
-#headers = ['#plugins/input/shape'] + env['CPPPATH']
 headers = env['CPPPATH']
 
 boost_program_options = 'boost_program_options%s' % env['BOOST_APPEND']
diff --git a/utils/shapeindex/build.py b/utils/shapeindex/build.py
index 9f7de7445..2a4c2ab07 100644
--- a/utils/shapeindex/build.py
+++ b/utils/shapeindex/build.py
@@ -25,7 +25,9 @@ from copy import copy
 
 Import ('env')
 
-program_env = env.Clone()
+Import ('plugin_base')
+
+program_env = plugin_base.Clone()
 
 source = Split(
     """