diff --git a/modules/Bio/EnsEMBL/Hive/Utils/Test.pm b/modules/Bio/EnsEMBL/Hive/Utils/Test.pm
index 7d014b347..fbfb772c5 100644
--- a/modules/Bio/EnsEMBL/Hive/Utils/Test.pm
+++ b/modules/Bio/EnsEMBL/Hive/Utils/Test.pm
@@ -199,20 +199,11 @@ sub init_pipeline {
         $url = (splice(@$options, $url_flag_index, 2))[1];
     }
 
-    local @ARGV = @$options;
-    unshift @ARGV, (-pipeline_url => $url, -hive_force_init => 1);
-
-    lives_ok(sub {
-        my $orig_unambig_url = Bio::EnsEMBL::Hive::Utils::URL::parse($url)->{'unambig_url'};
-        ok($orig_unambig_url, 'Given URL could be parsed');
-        my $returned_url = Bio::EnsEMBL::Hive::Scripts::InitPipeline::init_pipeline($file_or_module, $tweaks);
-        ok($returned_url, 'pipeline initialized on '.$returned_url);
-
-        my $returned_unambig_url = Bio::EnsEMBL::Hive::Utils::URL::parse($returned_url)->{'unambig_url'};
-            # Both $url and $returned_url MAY contain the password (if applicable for the driver) but can be missing the port number assuming a default
-            # Both $orig_unambig_url and $returned_unambig_url SHOULD contain the port number (if applicable for the driver) but WILL NOT contain a password
-        is($returned_unambig_url, $orig_unambig_url, 'pipeline initialized on '.$url);
-    }, sprintf('init_pipeline("%s", %s)', $file_or_module, stringify($options)));
+    my @args = ($file_or_module, -pipeline_url => $url, -hive_force_init => 1);
+    push @args, @$options;
+    push @args, map {-tweak => $_} @$tweaks if $tweaks;
+
+    return _test_ehive_script('init_pipeline', undef, \@args);
 }
 
 
diff --git a/t/02.api/fetch_and_count_by_multiple_columns.t b/t/02.api/fetch_and_count_by_multiple_columns.t
index b4da6290a..18d3bb3e7 100755
--- a/t/02.api/fetch_and_count_by_multiple_columns.t
+++ b/t/02.api/fetch_and_count_by_multiple_columns.t
@@ -37,7 +37,7 @@ my $ehive_test_pipeline_urls = get_test_urls();
 foreach my $pipeline_url (@$ehive_test_pipeline_urls) {
 
 subtest 'Test on '.$pipeline_url, sub {
-    plan tests => 20;
+    plan tests => 17;
 
 init_pipeline('Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMult_conf', $pipeline_url);
 
diff --git a/t/03.scripts/generate_graph.t b/t/03.scripts/generate_graph.t
index 3a277fba5..07c7bdf7d 100755
--- a/t/03.scripts/generate_graph.t
+++ b/t/03.scripts/generate_graph.t
@@ -39,10 +39,14 @@ GetOptions(
 
 my $server_url  = get_test_url_or_die(-tag => 'server', -no_user_prefix => 1);
 
-# Most of the test scripts test init_pipeline() from Utils::Test but we
-# also need to test the main scripts/init_pipeline.pl !
-my @init_pipeline_args = ($ENV{'EHIVE_ROOT_DIR'}.'/scripts/init_pipeline.pl', 'Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMultServer_conf', -pipeline_url => $server_url, -hive_force_init => 1, -tweak => 'pipeline.param[take_time]=0');
-test_command(\@init_pipeline_args);
+init_pipeline(
+    'Bio::EnsEMBL::Hive::Examples::LongMult::PipeConfig::LongMultServer_conf',
+    $server_url,
+    [],
+    [
+        'pipeline.param[take_time]=0',
+    ],
+);
 
 
 my $client_url  = get_test_url_or_die(-tag => 'client', -no_user_prefix => 1);
@@ -59,12 +63,6 @@ push @confs_to_test, 'GC::PipeConfig::GCPct_conf' unless $@;    # SKIP it in cas
 my ($fh, $tmp_filename) = tempfile(UNLINK => 1);
 close($fh);
 
-sub test_command {
-    my $cmd_array = shift;
-    ok(!system(@$cmd_array), 'Can run '.join(' ', @$cmd_array));
-}
-
-
 foreach my $conf (@confs_to_test) {
   subtest $conf, sub {
     my $module_name = 'Bio::EnsEMBL::Hive::Examples::'.$conf;
diff --git a/t/10.pipeconfig/analysis_heir.t b/t/10.pipeconfig/analysis_heir.t
index 7e516c024..79ab9c190 100755
--- a/t/10.pipeconfig/analysis_heir.t
+++ b/t/10.pipeconfig/analysis_heir.t
@@ -32,8 +32,7 @@ $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Fil
 my $pipeline_url = get_test_url_or_die();
 
 my $init_stderr = capture_stderr {
-    local @INC = @INC;
-    push @INC, $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/';
+    local $ENV{'PERL5LIB'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB};
     init_pipeline(
         'TestPipeConfig::MissingAnalysis_conf',
         $pipeline_url,
diff --git a/t/10.pipeconfig/gc_dataflow.t b/t/10.pipeconfig/gc_dataflow.t
index bf7d5cbb7..5d40e8051 100755
--- a/t/10.pipeconfig/gc_dataflow.t
+++ b/t/10.pipeconfig/gc_dataflow.t
@@ -30,8 +30,7 @@ $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Fil
 my $pipeline_url  = get_test_url_or_die();
 
 {
-    local @INC = @INC;
-    push @INC, $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/';
+    local $ENV{'PERL5LIB'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB};
     init_pipeline('TestPipeConfig::AnyFailureBranch_conf', $pipeline_url, [], ['pipeline.param[take_time]=100']);
 }
 my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $pipeline_url );
diff --git a/t/10.pipeconfig/pipeline_url.t b/t/10.pipeconfig/pipeline_url.t
index 46a4d0683..4dc4032af 100755
--- a/t/10.pipeconfig/pipeline_url.t
+++ b/t/10.pipeconfig/pipeline_url.t
@@ -21,7 +21,7 @@ use warnings;
 
 use Test::More;
 
-use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline beekeeper get_test_url_or_die safe_drop_database);
+use Bio::EnsEMBL::Hive::Utils::Test qw(init_pipeline get_test_url_or_die safe_drop_database);
 use Bio::EnsEMBL::Hive::Utils qw(destringify);
 
 # eHive needs this to initialize the pipeline (and run db_cmd.pl)
@@ -29,11 +29,10 @@ $ENV{'EHIVE_ROOT_DIR'} ||= File::Basename::dirname( File::Basename::dirname( Fil
 
 my $pipeline_url  = get_test_url_or_die();
 
-# Utils::Test::init_pipeline runs things internally instead of invoking init_pipeline.pl
-# Here we need to run the script to trigger the password sanitization
-my @cmd = ('env', 'PERL5LIB='.$ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB}, $ENV{'EHIVE_ROOT_DIR'}.'/scripts/init_pipeline.pl', 'TestPipeConfig::PipelineURL_conf', -pipeline_url => $pipeline_url);
-my $rc = system(@cmd);
-is($rc, 0, 'init_pipeline.pl successfully ran');
+{
+    local $ENV{'PERL5LIB'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/10.pipeconfig/::'.$ENV{PERL5LIB};
+    init_pipeline('TestPipeConfig::PipelineURL_conf', $pipeline_url);
+}
 
 my $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new( -url => $pipeline_url );