diff --git a/jenkins.sh b/jenkins.sh
index 0018ca610..7075b1a51 100755
--- a/jenkins.sh
+++ b/jenkins.sh
@@ -5,9 +5,10 @@ export PYTHONDONTWRITEBYTECODE=yep
 # Output test results as junit xml
 export TRIAL_FLAGS="--reporter=subunit"
 export TOXSUFFIX="| subunit-1to2 | subunit2junitxml --no-passthrough --output-to=results.xml"
-
-# Output coverage to coverage.xml
-export DUMP_COVERAGE_COMMAND="coverage xml -o coverage.xml"
+# Write coverage reports to a separate file for each process
+# Include branch coverage
+export COVERAGE_OPTS="-p"
+export DUMP_COVERAGE_COMMAND="coverage help"
 
 # Output flake8 violations to violations.flake8.log
 # Don't exit with non-0 status code on Jenkins,
@@ -15,6 +16,8 @@ export DUMP_COVERAGE_COMMAND="coverage xml -o coverage.xml"
 # UNSTABLE or FAILURE this build.
 export PEP8SUFFIX="--output-file=violations.flake8.log || echo flake8 finished with status code \$?"
 
+rm .coverage.* || echo "No files to remove"
+
 tox
 
 : ${GIT_BRANCH:="origin/$(git rev-parse --abbrev-ref HEAD)"}
@@ -45,7 +48,7 @@ export PERL5LIB PERL_MB_OPT PERL_MM_OPT
 : ${PORT_BASE:=8000}
 
 echo >&2 "Running sytest with SQLite3";
-./run-tests.pl -O tap --synapse-directory .. --all --port-base $PORT_BASE > results-sqlite3.tap
+./run-tests.pl --coverage -O tap --synapse-directory .. --all --port-base $PORT_BASE > results-sqlite3.tap
 
 RUN_POSTGRES=""
 
@@ -64,7 +67,15 @@ done
 if test $RUN_POSTGRES = ":$(($PORT_BASE + 1)):$(($PORT_BASE + 2))"; then
     echo >&2 "Running sytest with PostgreSQL";
     pip install psycopg2
-    ./run-tests.pl -O tap --synapse-directory .. --all --port-base $PORT_BASE > results-postgresql.tap
+    ./run-tests.pl --coverage -O tap --synapse-directory .. --all --port-base $PORT_BASE > results-postgresql.tap
 else
     echo >&2 "Skipping running sytest with PostgreSQL, $RUN_POSTGRES"
 fi
+
+cd ..
+cp sytest/.coverage.* .
+
+# Combine the coverage reports
+python -m coverage combine
+# Output coverage to coverage.xml
+coverage xml -o coverage.xml
diff --git a/tox.ini b/tox.ini
index 95424765c..bd313a4f3 100644
--- a/tox.ini
+++ b/tox.ini
@@ -11,7 +11,8 @@ deps =
 setenv =
     PYTHONDONTWRITEBYTECODE = no_byte_code
 commands =
-    /bin/bash -c "coverage run --source=synapse {envbindir}/trial {env:TRIAL_FLAGS:} {posargs:tests} {env:TOXSUFFIX:}"
+    /bin/bash -c "coverage run {env:COVERAGE_OPTS:} --source={toxinidir}/synapse \
+        {envbindir}/trial {env:TRIAL_FLAGS:} {posargs:tests} {env:TOXSUFFIX:}"
     {env:DUMP_COVERAGE_COMMAND:coverage report -m}
 
 [testenv:packaging]