diff --git a/test/system/104-run.bats b/test/system/104-run.bats
index 576d45c..d00fc2e 100644
--- a/test/system/104-run.bats
+++ b/test/system/104-run.bats
@@ -105,9 +105,10 @@ teardown() {
 @test "run: Try to run a command in the default container with no containers created" {
   local default_container_name="$(get_system_id)-toolbox-$(get_system_version)"
 
-  run $TOOLBOX run true
+  run --separate-stderr $TOOLBOX run true
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: container $default_container_name not found"
   assert_line --index 1 "Use the 'create' command to create a toolbox."
   assert_line --index 2 "Run 'toolbox --help' for usage."
@@ -118,9 +119,10 @@ teardown() {
 
   create_container other-container
 
-  run $TOOLBOX run true
+  run --separate-stderr $TOOLBOX run true
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: container $default_container_name not found"
   assert_line --index 1 "Use the 'create' command to create a toolbox."
   assert_line --index 2 "Run 'toolbox --help' for usage."
@@ -129,9 +131,10 @@ teardown() {
 @test "run: Try to run a command in a specific non-existent container" {
   create_container other-container
 
-  run $TOOLBOX run -c wrong-container true
+  run --separate-stderr $TOOLBOX run -c wrong-container true
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: container wrong-container not found"
   assert_line --index 1 "Use the 'create' command to create a toolbox."
   assert_line --index 2 "Run 'toolbox --help' for usage."
@@ -140,57 +143,63 @@ teardown() {
 @test "run: Try to run a command in a container based on unsupported distribution" {
   local distro="foo"
 
-  run $TOOLBOX --assumeyes run --distro "$distro" ls
+  run --separate-stderr $TOOLBOX --assumeyes run --distro "$distro" ls
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: invalid argument for '--distro'"
   assert_line --index 1 "Distribution $distro is unsupported."
   assert_line --index 2 "Run 'toolbox --help' for usage."
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 }
 
 @test "run: Try to run a command in a container based on Fedora but with wrong version" {
-  run $TOOLBOX run -d fedora -r foobar ls
+  run --separate-stderr $TOOLBOX run -d fedora -r foobar ls
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: invalid argument for '--release'"
   assert_line --index 1 "The release must be a positive integer."
   assert_line --index 2 "Run 'toolbox --help' for usage."
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 
-  run $TOOLBOX run --distro fedora --release -3 ls
+  run --separate-stderr $TOOLBOX run --distro fedora --release -3 ls
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: invalid argument for '--release'"
   assert_line --index 1 "The release must be a positive integer."
   assert_line --index 2 "Run 'toolbox --help' for usage."
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 }
 
 @test "run: Try to run a command in a container based on RHEL but with wrong version" {
-  run $TOOLBOX run --distro rhel --release 8 ls
+  run --separate-stderr $TOOLBOX run --distro rhel --release 8 ls
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: invalid argument for '--release'"
   assert_line --index 1 "The release must be in the '<major>.<minor>' format."
   assert_line --index 2 "Run 'toolbox --help' for usage."
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 
-  run $TOOLBOX run --distro rhel --release 8.2foo ls
+  run --separate-stderr $TOOLBOX run --distro rhel --release 8.2foo ls
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: invalid argument for '--release'"
   assert_line --index 1 "The release must be in the '<major>.<minor>' format."
   assert_line --index 2 "Run 'toolbox --help' for usage."
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 
-  run $TOOLBOX run --distro rhel --release -2.1 ls
+  run --separate-stderr $TOOLBOX run --distro rhel --release -2.1 ls
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: invalid argument for '--release'"
   assert_line --index 1 "The release must be a positive number."
   assert_line --index 2 "Run 'toolbox --help' for usage."
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 }
 
 @test "run: Try to run a command in a container based on non-default distro without providing a version" {
@@ -201,13 +210,14 @@ teardown() {
     distro="rhel"
   fi
 
-  run $TOOLBOX run -d "$distro" ls
+  run --separate-stderr $TOOLBOX run -d "$distro" ls
 
   assert_failure
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "Error: option '--release' is needed"
   assert_line --index 1 "Distribution $distro doesn't match the host."
   assert_line --index 2 "Run 'toolbox --help' for usage."
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 }
 
 @test "run: Run command exiting with non-zero code in the default container" {
@@ -224,26 +234,28 @@ teardown() {
 
   create_default_container
 
-  run -127 $TOOLBOX run $cmd
+  run -127 --separate-stderr $TOOLBOX run $cmd
 
   assert_failure
   assert [ $status -eq 127 ]
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "bash: line 1: exec: $cmd: not found"
   assert_line --index 1 "Error: command $cmd not found in container $(get_latest_container_name)"
-  assert [ ${#lines[@]} -eq 2 ]
+  assert [ ${#stderr_lines[@]} -eq 2 ]
 }
 
 @test "run: Try to run /etc as a command in the deault container" {
   create_default_container
 
-  run $TOOLBOX run /etc
+  run --separate-stderr $TOOLBOX run /etc
 
   assert_failure
   assert [ $status -eq 126 ]
+  lines=("${stderr_lines[@]}")
   assert_line --index 0 "bash: line 1: /etc: Is a directory"
   assert_line --index 1 "bash: line 1: exec: /etc: cannot execute: Is a directory"
   assert_line --index 2 "Error: failed to invoke command /etc in container $(get_latest_container_name)"
-  assert [ ${#lines[@]} -eq 3 ]
+  assert [ ${#stderr_lines[@]} -eq 3 ]
 }
 
 @test "run: Pass down 1 invalid file descriptor" {