diff --git a/test/functional/tools/job_environment_default.xml b/test/functional/tools/job_environment_default.xml
index 700e4419432f..4ce47e1680d8 100644
--- a/test/functional/tools/job_environment_default.xml
+++ b/test/functional/tools/job_environment_default.xml
@@ -12,8 +12,8 @@ echo \$(pwd) > '$pwd' &&
 echo "\$HOME" > '$home' &&
 echo "\$TMP"  > '$tmp' &&
 echo "\$SOME_ENV_VAR" > '$some_env_var' &&
-echo "\$JOBCONF_ENV_VAR" > '$jobconf_env_var' &&
-echo "\$CONTAINER_ENV_VAR" > '$container_env_var' &&
+echo "\${JOBCONF_ENV_VAR:-UNSET}" > '$jobconf_env_var' &&
+echo "\${CONTAINER_ENV_VAR:-UNSET}" > '$container_env_var' &&
 touch "\$_GALAXY_JOB_TMP_DIR/tmp_test" &&
 touch "\$HOME/home_test" &&
 
diff --git a/test/functional/tools/job_environment_default_legacy.xml b/test/functional/tools/job_environment_default_legacy.xml
index 6a2fec19d6d1..b63972fa642b 100644
--- a/test/functional/tools/job_environment_default_legacy.xml
+++ b/test/functional/tools/job_environment_default_legacy.xml
@@ -10,8 +10,8 @@ echo \$(pwd) > '$pwd' &&
 echo "\$HOME" > '$home' &&
 echo "\$TMP"  > '$tmp' &&
 echo "\$SOME_ENV_VAR" > '$some_env_var' &&
-echo "\$JOBCONF_ENV_VAR" > '$jobconf_env_var' &&
-echo "\$CONTAINER_ENV_VAR" > '$container_env_var' &&
+echo "\${JOBCONF_ENV_VAR:-UNSET}" > '$jobconf_env_var' &&
+echo "\${CONTAINER_ENV_VAR:-UNSET}" > '$container_env_var' &&
 
 touch "\${TMP:-/tmp}/job_tmp" &&
 touch "\${TEMP:-/tmp}/job_temp" &&
diff --git a/test/functional/tools/job_environment_explicit_isolated_home.xml b/test/functional/tools/job_environment_explicit_isolated_home.xml
index d09713595dff..48f5ed2398aa 100644
--- a/test/functional/tools/job_environment_explicit_isolated_home.xml
+++ b/test/functional/tools/job_environment_explicit_isolated_home.xml
@@ -10,7 +10,8 @@ echo \$(pwd) > '$pwd' &&
 echo "\$HOME" > '$home' &&
 echo "\$TMP"  > '$tmp' &&
 echo "\$SOME_ENV_VAR" > '$some_env_var' &&
-echo "\$JOBCONF_ENV_VAR" > '$jobconf_env_var' &&
+echo "\${JOBCONF_ENV_VAR:-UNSET}" > '$jobconf_env_var' &&
+echo "\${CONTAINER_ENV_VAR:-UNSET}" > '$container_env_var' &&
 
 touch "\${TMP:-/tmp}/job_tmp" &&
 touch "\${TEMP:-/tmp}/job_temp" &&
@@ -26,6 +27,7 @@ touch "\${TMPDIR:-/tmp}/job_tmpdir"
         <data name="tmp" format="txt" label="tmp" />
         <data name="some_env_var" format="txt" label="env_var" />
         <data name="jobconf_env_var" format="txt" label="jobconf_env_var" />
+        <data name="container_env_var" format="txt" label="container_env_var" />
     </outputs>
     <tests>
     </tests>
diff --git a/test/functional/tools/job_environment_explicit_shared_home.xml b/test/functional/tools/job_environment_explicit_shared_home.xml
index 680981dfb449..bf7bb101d0f8 100644
--- a/test/functional/tools/job_environment_explicit_shared_home.xml
+++ b/test/functional/tools/job_environment_explicit_shared_home.xml
@@ -10,7 +10,8 @@ echo \$(pwd) > '$pwd' &&
 echo "\$HOME" > '$home' &&
 echo "\$TMP"  > '$tmp' &&
 echo "\$SOME_ENV_VAR" > '$some_env_var' &&
-echo "\$JOBCONF_ENV_VAR" > '$jobconf_env_var' &&
+echo "\${JOBCONF_ENV_VAR:-UNSET}" > '$jobconf_env_var' &&
+echo "\${CONTAINER_ENV_VAR:-UNSET}" > '$container_env_var' &&
 
 touch "\${TMP:-/tmp}/job_tmp" &&
 touch "\${TEMP:-/tmp}/job_temp" &&
@@ -26,6 +27,7 @@ touch "\${TMPDIR:-/tmp}/job_tmpdir"
         <data name="tmp" format="txt" label="tmp" />
         <data name="some_env_var" format="txt" label="env_var" />
         <data name="jobconf_env_var" format="txt" label="jobconf_env_var" />
+        <data name="container_env_var" format="txt" label="container_env_var" />
     </outputs>
     <tests>
     </tests>
diff --git a/test/integration/dockerized_job_conf.yml b/test/integration/dockerized_job_conf.yml
index 5c8c37a35604..5b17eb57ae51 100644
--- a/test/integration/dockerized_job_conf.yml
+++ b/test/integration/dockerized_job_conf.yml
@@ -14,7 +14,7 @@ execution:
           value: 'YEAH'
         - execute: 'true' # just check that this does not confuse env setup
       docker_enabled: true
-      docker_env_CONTAINER_VAR: "DOCKER_VAR_VALUE"
+      docker_env_CONTAINER_ENV_VAR: "CONTAINER_VAR_VALUE"
       require_container: true
       tmp_dir: '$(mktemp -d)'
     local_docker_inline_container_resolvers:
diff --git a/test/integration/simple_job_conf.xml b/test/integration/simple_job_conf.xml
index 032c2b0fec16..649170f2ff64 100644
--- a/test/integration/simple_job_conf.xml
+++ b/test/integration/simple_job_conf.xml
@@ -10,6 +10,9 @@
 
     <destinations>
         <destination id="local_dest" runner="local">
+            <env id="JOBCONF_ENV_VAR">YEAH</env>
+            <param id="docker_env_CONTAINER_VAR">CONTAINER_VAR_VALUE</param>
+            <param id="singularity_env_CONTAINER_VAR">CONTAINER_VAR_VALUE</param>
         </destination>
     </destinations>
 
diff --git a/test/integration/singularity_job_conf.yml b/test/integration/singularity_job_conf.yml
index 8ea57e90ab58..6f5e4f182c86 100644
--- a/test/integration/singularity_job_conf.yml
+++ b/test/integration/singularity_job_conf.yml
@@ -13,7 +13,7 @@ execution:
         - name: 'JOBCONF_ENV_VAR'
           value: 'YEAH'
       singularity_enabled: true
-      singularity_env_CONTAINER_VAR: "SINGULARITY_VAR_VALUE"
+      singularity_env_CONTAINER_ENV_VAR: "CONTAINER_VAR_VALUE"
       # Since tests run in /tmp/ , we apparently need to forbid the default mounting of /tmp
       singularity_run_extra_arguments: '--no-mount tmp'
       require_container: true
diff --git a/test/integration/test_containerized_jobs.py b/test/integration/test_containerized_jobs.py
index 4c7f784456c5..24967c1862b3 100644
--- a/test/integration/test_containerized_jobs.py
+++ b/test/integration/test_containerized_jobs.py
@@ -122,7 +122,8 @@ def test_container_job_environment(self) -> None:
         assert job_env.pwd.endswith("/working")
         assert job_env.home.startswith(self.jobs_directory)
         assert job_env.home.endswith("/home")
-        assert job_env.jobconf_env_var == "YEAH"
+        assert job_env.jobconf_env_var == "UNSET"
+        assert job_env.container_env_var == "CONTAINER_VAR_VALUE"
 
     def test_container_job_environment_legacy(self) -> None:
         """
@@ -140,7 +141,8 @@ def test_container_job_environment_legacy(self) -> None:
         assert job_env.pwd.endswith("/working")
         assert not job_env.home.startswith(self.jobs_directory)
         assert not job_env.home.endswith("/home")
-        assert job_env.jobconf_env_var == "YEAH"
+        assert job_env.jobconf_env_var == "UNSET"
+        assert job_env.container_env_var == "CONTAINER_VAR_VALUE"
 
     def test_container_job_environment_explicit_shared_home(self) -> None:
         """
@@ -153,7 +155,8 @@ def test_container_job_environment_explicit_shared_home(self) -> None:
         assert job_env.pwd.endswith("/working")
         assert not job_env.home.startswith(self.jobs_directory)
         assert not job_env.home.endswith("/home"), job_env.home
-        assert job_env.jobconf_env_var == "YEAH"
+        assert job_env.jobconf_env_var == "UNSET"
+        assert job_env.container_env_var == "CONTAINER_VAR_VALUE"
 
     def test_container_job_environment_explicit_isolated_home(self) -> None:
         """
@@ -166,7 +169,8 @@ def test_container_job_environment_explicit_isolated_home(self) -> None:
         assert job_env.pwd.endswith("/working")
         assert job_env.home.startswith(self.jobs_directory)
         assert job_env.home.endswith("/home"), job_env.home
-        assert job_env.jobconf_env_var == "YEAH"
+        assert job_env.jobconf_env_var == "UNSET"
+        assert job_env.container_env_var == "CONTAINER_VAR_VALUE"
 
     def test_build_mulled(self) -> None:
         """
diff --git a/test/integration/test_job_environments.py b/test/integration/test_job_environments.py
index 100b5c532c05..d3bb0c4485ee 100644
--- a/test/integration/test_job_environments.py
+++ b/test/integration/test_job_environments.py
@@ -63,7 +63,7 @@ def _environment_properties(self, history_id):
         tmp = self.dataset_populator.get_history_dataset_content(history_id, hid=5).strip()
         some_env = self.dataset_populator.get_history_dataset_content(history_id, hid=6).strip()
         jobconf_env_var = self.dataset_populator.get_history_dataset_content(history_id, hid=7).strip()
-        container_env_var = self.dataset_populator.get_history_dataset_content(history_id, hid=7).strip()
+        container_env_var = self.dataset_populator.get_history_dataset_content(history_id, hid=8).strip()
         return JobEnvironmentProperties(user_id, group_id, pwd, home, tmp, some_env, jobconf_env_var, container_env_var)
 
     def _check_completed_history(self, history_id):
@@ -92,6 +92,10 @@ def test_default_environment_1801(self):
         assert job_env.pwd.startswith(self.jobs_directory)
         assert job_env.pwd.endswith("/working")
 
+        # check that env variables job
+        assert job_env.jobconf_env_var =="YEAH"
+        assert job_env.container_env_var =="UNSET"
+
         # Newer tools get isolated home directories in job_directory/home
         job_directory = os.path.dirname(job_env.pwd)
         assert job_env.home == os.path.join(job_directory, "home"), job_env.home