diff --git a/src/lib/Hydra/Plugin/BitBucketPulls.pm b/src/lib/Hydra/Plugin/BitBucketPulls.pm
index cb26da30..8e7a087a 100644
--- a/src/lib/Hydra/Plugin/BitBucketPulls.pm
+++ b/src/lib/Hydra/Plugin/BitBucketPulls.pm
@@ -10,6 +10,7 @@ use Hydra::Helper::CatalystUtils;
 use Hydra::Helper::Nix;
 use File::Temp;
 use POSIX qw(strftime);
+use IPC::Run qw(run);
 
 sub supportedInputTypes {
     my ($self, $inputTypes) = @_;
@@ -48,7 +49,7 @@ sub fetchInput {
     open(my $fh, ">", $filename) or die "Cannot open $filename for writing: $!";
     print $fh encode_json \%pulls;
     close $fh;
-    system("jq -S . < $filename > $tempdir/bitbucket-pulls-sorted.json");
+    run(["jq", "-S", "."], '<', $filename, '>', "$tempdir/bitbucket-pulls-sorted.json") or die "jq command failed: $?";
     my $storePath = addToStore("$tempdir/bitbucket-pulls-sorted.json");
     my $timestamp = time;
     return { storePath => $storePath, revision => strftime "%Y%m%d%H%M%S", gmtime($timestamp) };
diff --git a/src/lib/Hydra/Plugin/GithubRefs.pm b/src/lib/Hydra/Plugin/GithubRefs.pm
index 1739204e..105c70ae 100644
--- a/src/lib/Hydra/Plugin/GithubRefs.pm
+++ b/src/lib/Hydra/Plugin/GithubRefs.pm
@@ -10,6 +10,7 @@ use Hydra::Helper::CatalystUtils;
 use Hydra::Helper::Nix;
 use File::Temp;
 use POSIX qw(strftime);
+use IPC::Run qw(run);
 
 =head1 NAME
 
@@ -115,7 +116,7 @@ sub fetchInput {
     open(my $fh, ">", $filename) or die "Cannot open $filename for writing: $!";
     print $fh encode_json \%refs;
     close $fh;
-    system("jq -S . < $filename > $tempdir/github-refs-sorted.json");
+    run(["jq", "-S", "."], '<', $filename, '>', "$tempdir/github-refs-sorted.json") or die "jq command failed: $?";
     my $storePath = addToStore("$tempdir/github-refs-sorted.json");
     my $timestamp = time;
     return { storePath => $storePath, revision => strftime "%Y%m%d%H%M%S", gmtime($timestamp) };
diff --git a/src/lib/Hydra/Plugin/GitlabPulls.pm b/src/lib/Hydra/Plugin/GitlabPulls.pm
index 2a31b1cf..b53d387e 100644
--- a/src/lib/Hydra/Plugin/GitlabPulls.pm
+++ b/src/lib/Hydra/Plugin/GitlabPulls.pm
@@ -24,6 +24,7 @@ use Hydra::Helper::CatalystUtils;
 use Hydra::Helper::Nix;
 use File::Temp;
 use POSIX qw(strftime);
+use IPC::Run qw(run);
 
 sub supportedInputTypes {
     my ($self, $inputTypes) = @_;
@@ -86,7 +87,7 @@ sub fetchInput {
     open(my $fh, ">", $filename) or die "Cannot open $filename for writing: $!";
     print $fh encode_json \%pulls;
     close $fh;
-    system("jq -S . < $filename > $tempdir/gitlab-pulls-sorted.json");
+    run(["jq", "-S", "."], '<', $filename, '>', "$tempdir/gitlab-pulls-sorted.json") or die "jq command failed: $?";
     my $storePath = addToStore("$tempdir/gitlab-pulls-sorted.json");
     my $timestamp = time;
     return { storePath => $storePath, revision => strftime "%Y%m%d%H%M%S", gmtime($timestamp) };
diff --git a/src/lib/Hydra/Plugin/S3Backup.pm b/src/lib/Hydra/Plugin/S3Backup.pm
index f1f50754..133b62d1 100644
--- a/src/lib/Hydra/Plugin/S3Backup.pm
+++ b/src/lib/Hydra/Plugin/S3Backup.pm
@@ -7,6 +7,8 @@ use File::Temp;
 use File::Basename;
 use Fcntl;
 use IO::File;
+use IPC::Run qw(run);
+use IPC::Run3;
 use Net::Amazon::S3;
 use Net::Amazon::S3::Client;
 use Digest::SHA;
@@ -27,11 +29,11 @@ my %compressors = ();
 $compressors{"none"} = "";
 
 if (defined($Nix::Config::bzip2)) {
-    $compressors{"bzip2"} = "| $Nix::Config::bzip2",
+    $compressors{"bzip2"} = "$Nix::Config::bzip2",
 }
 
 if (defined($Nix::Config::xz)) {
-    $compressors{"xz"} = "| $Nix::Config::xz",
+    $compressors{"xz"} = "$Nix::Config::xz",
 }
 
 my $lockfile = Hydra::Model::DB::getHydraPath . "/.hydra-s3backup.lock";
@@ -111,7 +113,16 @@ sub buildFinished {
             }
             next unless @incomplete_buckets;
             my $compressor = $compressors{$compression_type};
-            system("$Nix::Config::binDir/nix-store --dump $path $compressor > $tempdir/nar") == 0 or die;
+            if ($compressor eq "") {
+                # No compression - use IPC::Run3 to redirect stdout to file
+                run3(["$Nix::Config::binDir/nix-store", "--dump", $path],
+                     \undef, "$tempdir/nar", \undef) or die "nix-store --dump failed: $!";
+            } else {
+                # With compression - use IPC::Run to pipe nix-store output to compressor
+                my $dump_cmd = ["$Nix::Config::binDir/nix-store", "--dump", $path];
+                my $compress_cmd = [$compressor];
+                run($dump_cmd, '|', $compress_cmd, '>', "$tempdir/nar") or die "Pipeline failed: $?";
+            }
             my $digest = Digest::SHA->new(256);
             $digest->addfile("$tempdir/nar");
             my $file_hash = $digest->hexdigest;
diff --git a/t/Hydra/Plugin/gitea.t b/t/Hydra/Plugin/gitea.t
index d84c8f57..3de4ea8f 100644
--- a/t/Hydra/Plugin/gitea.t
+++ b/t/Hydra/Plugin/gitea.t
@@ -50,7 +50,7 @@ my $pid;
 if (!defined($pid = fork())) {
     die "Cannot fork(): $!";
 } elsif ($pid == 0) {
-    exec("python3 $ctx{jobsdir}/server.py $filename");
+    exec("python3", "$ctx{jobsdir}/server.py", $filename);
 } else {
     my $newbuild = $db->resultset('Builds')->find($build->id);
     is($newbuild->finished, 1, "Build should be finished.");
diff --git a/t/s3-backup-test.pl b/t/s3-backup-test.pl
index a367981f..3132571e 100644
--- a/t/s3-backup-test.pl
+++ b/t/s3-backup-test.pl
@@ -19,11 +19,11 @@ my $jobsetinput;
 
 $jobsetinput = $jobset->jobsetinputs->create({name => "jobs", type => "path"});
 $jobsetinput->jobsetinputalts->create({altnr => 0, value => getcwd . "/jobs"});
-system("hydra-eval-jobset " . $jobset->project->name . " " . $jobset->name);
+system("hydra-eval-jobset", $jobset->project->name, $jobset->name);
 
 my $successful_hash;
 foreach my $build ($jobset->builds->search({finished => 0})) {
-    system("hydra-build " . $build->id);
+    system("hydra-build", $build->id);
     my @outputs = $build->buildoutputs->all;
     my $hash = substr basename($outputs[0]->path), 0, 32;
     if ($build->job->name eq "job") {