diff --git a/CHANGELOG.md b/CHANGELOG.md
index 58a9f6c..941416d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,16 @@
 
 All notable changes to `atb-cli` are documented here. Format follows [Keep a Changelog](https://keepachangelog.com/).
 
+## [Unreleased]
+
+### Fixed
+
+- Every error was printed twice. Cobra wrote the `Error: ...` line when a
+  command returned and `main` wrote the same sentence again, so one failure
+  looked like two. The error is now reported once, keeping the `Error: ` prefix
+  that separates it from the progress and warning output `atb` also writes to
+  stderr. Exit codes are unchanged.
+
 ## [v0.21.0](https://github.com/allthebacteria/atb-cli/releases/tag/v0.21.0) - 2026-08-05
 
 ### Added
diff --git a/cmd/atb/main.go b/cmd/atb/main.go
index 664b78e..f1aec81 100644
--- a/cmd/atb/main.go
+++ b/cmd/atb/main.go
@@ -2,8 +2,11 @@ package main
 
 import (
 	"fmt"
+	"io"
 	"os"
 
+	"github.com/spf13/cobra"
+
 	"github.com/allthebacteria/atb-cli/internal/cli"
 )
 
@@ -12,7 +15,13 @@ var version = "dev"
 
 func main() {
 	cli.RootCmd.Version = version
-	err := cli.RootCmd.Execute()
+	os.Exit(run(cli.RootCmd, os.Stderr))
+}
+
+// run executes root and returns the process exit code, reporting any error on
+// stderr.
+func run(root *cobra.Command, stderr io.Writer) int {
+	err := root.Execute()
 
 	// Let the background update check finish saving state (up to 2s).
 	if cli.WaitForUpdateCheck != nil {
@@ -20,7 +29,8 @@ func main() {
 	}
 
 	if err != nil {
-		fmt.Fprintln(os.Stderr, err)
-		os.Exit(1)
+		fmt.Fprintln(stderr, "Error:", err)
+		return 1
 	}
+	return 0
 }
diff --git a/cmd/atb/main_test.go b/cmd/atb/main_test.go
new file mode 100644
index 0000000..1474b49
--- /dev/null
+++ b/cmd/atb/main_test.go
@@ -0,0 +1,67 @@
+package main
+
+import (
+	"bytes"
+	"strings"
+	"testing"
+
+	"github.com/spf13/cobra"
+
+	"github.com/allthebacteria/atb-cli/internal/cli"
+)
+
+// failingRoot builds a real command tree and an argument list that always
+// fails during flag parsing, so the test does not depend on any data files.
+func failingRoot() (*cobra.Command, *bytes.Buffer) {
+	root := cli.NewRootCmd("test")
+	root.SetArgs([]string{"query", "--no-such-flag"})
+
+	var out bytes.Buffer
+	root.SetOut(&out)
+	root.SetErr(&out)
+	return root, &out
+}
+
+// Cobra reports the error when Execute returns and main reported it a second
+// time, so the same sentence reached the user twice.
+func TestRunReportsAnErrorOnce(t *testing.T) {
+	root, out := failingRoot()
+
+	code := run(root, out)
+
+	if code != 1 {
+		t.Errorf("exit code: got %d, want 1", code)
+	}
+	if got := strings.Count(out.String(), "unknown flag: --no-such-flag"); got != 1 {
+		t.Errorf("error reported %d time(s), want 1:\n%s", got, out.String())
+	}
+}
+
+// atb writes progress and warnings to stderr as well, so the error keeps the
+// conventional prefix that separates it from that output.
+func TestRunPrefixesTheError(t *testing.T) {
+	root, out := failingRoot()
+
+	run(root, out)
+
+	line := strings.TrimSpace(out.String())
+	if !strings.HasPrefix(line, "Error: ") {
+		t.Errorf("error line should start with %q, got:\n%s", "Error: ", line)
+	}
+}
+
+func TestRunReportsNothingOnSuccess(t *testing.T) {
+	root := cli.NewRootCmd("test")
+	root.SetArgs([]string{"--help"})
+
+	var out bytes.Buffer
+	root.SetOut(&out)
+	root.SetErr(&out)
+
+	if code := run(root, &out); code != 0 {
+		t.Errorf("exit code: got %d, want 0", code)
+	}
+	if strings.Contains(out.String(), "Error:") {
+		t.Errorf("--help should not report an error, got:\n%s", out.String())
+	}
+}
diff --git a/internal/cli/root.go b/internal/cli/root.go
index 517f93f..f16835c 100644
--- a/internal/cli/root.go
+++ b/internal/cli/root.go
@@ -26,10 +26,14 @@ var (
 )
 
 // RootCmd is the base command for atb.
+//
+// SilenceErrors leaves reporting to main, which prints the error after the
+// background update check has finished writing to stderr.
 var RootCmd = &cobra.Command{
-	Use:          "atb",
-	Short:        "Query and download AllTheBacteria genomes",
-	SilenceUsage: true,
+	Use:           "atb",
+	Short:         "Query and download AllTheBacteria genomes",
+	SilenceUsage:  true,
+	SilenceErrors: true,
 }
 
 func init() {
@@ -69,10 +73,11 @@ func NewRootCmd(version string) *cobra.Command {
 	var localCfgFile, localDataDir string
 
 	root := &cobra.Command{
-		Use:          "atb",
-		Short:        "Query and download AllTheBacteria genomes",
-		SilenceUsage: true,
-		Version:      version,
+		Use:           "atb",
+		Short:         "Query and download AllTheBacteria genomes",
+		SilenceUsage:  true,
+		SilenceErrors: true,
+		Version:       version,
 	}
 
 	root.PersistentFlags().StringVar(&localCfgFile, "config", "", "config file (default $HOME/.atb/config.toml)")