diff --git a/.circleci/config.yml b/.circleci/config.yml
index 9749d524e8d..b1a3aae3675 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -374,7 +374,7 @@ _steps:
         codecov_version=$(grep -o 'VERSION=\"[0-9\.]*\"' codecov | cut -d'"' -f2)
         shasum -a 512 -c <(curl -s "https://raw.githubusercontent.com/codecov/codecov-bash/${codecov_version}/SHA512SUM" | grep -w "codecov")
         bash codecov \
-          -f "lcov/total_coverage.info" \
+          -f "lcov/project_coverage.info" \
           -R "src/navigation2" \
           -F "project" \
           -Z || echo 'Codecov upload failed'
diff --git a/Dockerfile b/Dockerfile
index 0523cbacc4d..37e72180997 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -63,7 +63,6 @@ RUN apt-get update && \
       ros-$ROS_DISTRO-rmw-connextdds \
       ros-$ROS_DISTRO-rmw-cyclonedds-cpp \
     && pip3 install \
-      fastcov \
       git+https://github.com/ruffsl/colcon-cache.git@c1cedadc1ac6131fe825d075526ed4ae8e1b473c \
       git+https://github.com/ruffsl/colcon-clean.git@87dee2dd1e47c2b97ac6d8300f76e3f607d19ef6 \
     && rosdep update \
diff --git a/tools/code_coverage_report.bash b/tools/code_coverage_report.bash
index ccc8220b91c..e836a3ed944 100755
--- a/tools/code_coverage_report.bash
+++ b/tools/code_coverage_report.bash
@@ -36,36 +36,64 @@ for opt in "$@" ; do
 done
 
 set -o xtrace
-mkdir -p ${LCOVDIR}
+mkdir -p $LCOVDIR
 
-# Ignore certain packages:
-# - messages, which are auto generated files
-# - system tests, which are themselves all test artifacts
-# - rviz plugins, which are not used for real navigation
-INCLUDE_PACKAGES=$(
-  colcon list \
-    --paths-only \
-    --packages-ignore-regex \
-      ".*_msgs" \
-      ".*_tests" \
-      ".*_rviz.*" \
-  | xargs)
+# Generate initial zero-coverage data.
+# This adds files that were otherwise not run to the report
+lcov --capture --initial \
+  --directory build \
+  --output-file ${LCOVDIR}/initial_coverage.info \
+  --rc lcov_branch_coverage=0
 
 # Capture executed code data.
-fastcov \
-  -d build \
-  --exclude test/ \
-  --include $INCLUDE_PACKAGES \
-  --output ${LCOVDIR}/total_coverage.info --lcov
+lcov --capture \
+  --directory build \
+  --output-file ${LCOVDIR}/test_coverage.info \
+  --rc lcov_branch_coverage=0
+
+# Combine the initial zero-coverage report with the executed lines report.
+lcov \
+  --add-tracefile ${LCOVDIR}/initial_coverage.info \
+  --add-tracefile ${LCOVDIR}/test_coverage.info \
+  --output-file ${LCOVDIR}/full_coverage.info \
+  --rc lcov_branch_coverage=0
+
+# Only include files that are within this workspace.
+# (eg filter out stdio.h etc)
+lcov \
+  --extract ${LCOVDIR}/full_coverage.info \
+    "${PWD}/*" \
+  --output-file ${LCOVDIR}/workspace_coverage.info \
+  --rc lcov_branch_coverage=0
+
+# Remove files in the build subdirectory.
+# Those are generated files (like messages, services, etc)
+# And system tests, which are themselves all test artifacts
+# And rviz plugins, which are not used for real navigation
+lcov \
+  --remove ${LCOVDIR}/workspace_coverage.info \
+    "${PWD}/build/*" \
+  --remove ${LCOVDIR}/workspace_coverage.info \
+    "${PWD}/*/dwb_msgs/*" \
+  --remove ${LCOVDIR}/workspace_coverage.info \
+    "${PWD}/*/nav2_msgs/*" \
+  --remove ${LCOVDIR}/workspace_coverage.info \
+    "${PWD}/*/nav_2d_msgs/*" \
+  --remove ${LCOVDIR}/workspace_coverage.info \
+    "${PWD}/*/nav2_system_tests/*" \
+  --remove ${LCOVDIR}/workspace_coverage.info \
+    "${PWD}/*/nav2_rviz_plugins/*" \
+  --output-file ${LCOVDIR}/project_coverage.info \
+  --rc lcov_branch_coverage=0
 
 if [ $COVERAGE_REPORT_VIEW = codecovio ]; then
   curl -s https://codecov.io/bash > codecov
   codecov_version=$(grep -o 'VERSION=\"[0-9\.]*\"' codecov | cut -d'"' -f2)
   shasum -a 512 -c <(curl -s "https://raw.githubusercontent.com/codecov/codecov-bash/${codecov_version}/SHA512SUM" | grep -w "codecov")
   bash codecov \
-    -f ${LCOVDIR}/total_coverage.info \
+    -f ${LCOVDIR}/project_coverage.info \
     -R src/navigation2
 elif [ $COVERAGE_REPORT_VIEW = genhtml ]; then
-  genhtml ${LCOVDIR}/total_coverage.info \
+  genhtml ${LCOVDIR}/project_coverage.info \
     --output-directory ${LCOVDIR}/html
 fi