diff --git a/cli/cmd/app_hostname_ls.go b/cli/cmd/app_hostname_ls.go
index 7e755e425..bd881d0c2 100644
--- a/cli/cmd/app_hostname_ls.go
+++ b/cli/cmd/app_hostname_ls.go
@@ -79,7 +79,7 @@ replicated app hostname ls --app myapp --output json`,
 func (r *runners) listAppHostnames(ctx context.Context, outputFormat string) error {
 	// Only show spinners for table output
 	showSpinners := outputFormat == "table"
-	log := logger.NewLogger(r.w)
+	log := logger.NewLogger(r.w).SetIsTerminal(r.stdoutIsTTY)
 
 	// Resolve app ID from slug or ID
 	appSlugOrID := r.appSlug
diff --git a/cli/cmd/app_rm.go b/cli/cmd/app_rm.go
index 6d3e4fbef..219b58be8 100644
--- a/cli/cmd/app_rm.go
+++ b/cli/cmd/app_rm.go
@@ -54,15 +54,22 @@ replicated app delete "Custom App" --output json`,
 }
 
 func (r *runners) deleteApp(ctx context.Context, cmd *cobra.Command, appName string, opts deleteAppOpts, outputFormat string) error {
-	log := logger.NewLogger(r.w)
+	log := logger.NewLogger(r.w).SetIsTerminal(r.stdoutIsTTY)
+	showSpinners := outputFormat == "table"
 
-	log.ActionWithSpinner("Fetching App")
+	if showSpinners {
+		log.ActionWithSpinner("Fetching App")
+	}
 	app, err := r.kotsAPI.GetApp(ctx, appName, true)
 	if err != nil {
-		log.FinishSpinnerWithError()
+		if showSpinners {
+			log.FinishSpinnerWithError()
+		}
 		return errors.Wrap(err, "list apps")
 	}
-	log.FinishSpinner()
+	if showSpinners {
+		log.FinishSpinner()
+	}
 
 	apps := []types.AppAndChannels{
 		{
@@ -86,13 +93,19 @@ func (r *runners) deleteApp(ctx context.Context, cmd *cobra.Command, appName str
 		}
 	}
 
-	log.ActionWithSpinner("Deleting App")
+	if showSpinners {
+		log.ActionWithSpinner("Deleting App")
+	}
 	err = r.kotsAPI.DeleteKOTSApp(ctx, app.ID)
 	if err != nil {
-		log.FinishSpinnerWithError()
+		if showSpinners {
+			log.FinishSpinnerWithError()
+		}
 		return errors.Wrap(err, "delete app")
 	}
-	log.FinishSpinner()
+	if showSpinners {
+		log.FinishSpinner()
+	}
 
 	return nil
 }
diff --git a/cli/cmd/cluster_kubeconfig.go b/cli/cmd/cluster_kubeconfig.go
index 88615e989..2fcf57421 100644
--- a/cli/cmd/cluster_kubeconfig.go
+++ b/cli/cmd/cluster_kubeconfig.go
@@ -108,7 +108,7 @@ func (r *runners) kubeconfigCluster(_ *cobra.Command, args []string) error {
 	}
 
 	if r.args.kubeconfigStdout {
-		fmt.Println(string(kubeconfig))
+		fmt.Print(string(kubeconfig))
 		return nil
 	}
 
@@ -123,7 +123,7 @@ func (r *runners) kubeconfigCluster(_ *cobra.Command, args []string) error {
 			return errors.Wrap(err, "write kubeconfig")
 		}
 
-		fmt.Printf("kubeconfig written to %s\n", r.args.kubeconfigPath)
+		fmt.Fprintf(os.Stderr, "kubeconfig written to %s\n", r.args.kubeconfigPath)
 		return nil
 	}
 
@@ -180,7 +180,7 @@ func (r *runners) kubeconfigCluster(_ *cobra.Command, args []string) error {
 		for _, backupPath := range backupPaths {
 			err := os.Remove(backupPath)
 			if err != nil {
-				fmt.Printf("failed to remove backup kubeconfig: %s\n", err.Error())
+				fmt.Fprintf(os.Stderr, "failed to remove backup kubeconfig: %s\n", err.Error())
 			}
 		}
 	}()
@@ -215,7 +215,7 @@ func (r *runners) kubeconfigCluster(_ *cobra.Command, args []string) error {
 		return errors.Wrap(err, "write kubeconfig")
 	}
 
-	fmt.Printf(" ✓  Updated kubernetes context '%s' in '%s'\n", mergedConfig.CurrentContext, kubeconfigPaths[0])
+	fmt.Fprintf(os.Stderr, " ✓  Updated kubernetes context '%s' in '%s'\n", mergedConfig.CurrentContext, kubeconfigPaths[0])
 
 	return nil
 }
diff --git a/cli/cmd/cluster_prepare.go b/cli/cmd/cluster_prepare.go
index e0affc2d7..965ad9de3 100644
--- a/cli/cmd/cluster_prepare.go
+++ b/cli/cmd/cluster_prepare.go
@@ -154,7 +154,7 @@ func (r *runners) prepareCluster(_ *cobra.Command, args []string) error {
 		return errors.New("no app specified")
 	}
 
-	log := logger.NewLogger(r.w)
+	log := logger.NewLogger(r.w).SetIsTerminal(r.stdoutIsTTY)
 
 	release, err := prepareRelease(r, log)
 	if err != nil {
diff --git a/cli/cmd/installer_create.go b/cli/cmd/installer_create.go
index 101c4b8ac..38ebf0256 100644
--- a/cli/cmd/installer_create.go
+++ b/cli/cmd/installer_create.go
@@ -58,7 +58,7 @@ func (r *runners) installerCreate(_ *cobra.Command, _ []string) error {
 		return errors.Errorf("Installer specs are only supported for KOTS applications, app %q has type %q", r.appID, r.appType)
 	}
 
-	log := logger.NewLogger(r.w)
+	log := logger.NewLogger(r.w).SetIsTerminal(r.stdoutIsTTY)
 	if r.args.createInstallerAutoDefaults {
 		log.ActionWithSpinner("Reading Environment")
 		err := r.setKOTSDefaultInstallerParams()
diff --git a/cli/cmd/lint.go b/cli/cmd/lint.go
index 3a18d8f24..1b4662d44 100644
--- a/cli/cmd/lint.go
+++ b/cli/cmd/lint.go
@@ -147,8 +147,12 @@ func (r *runners) runLint(cmd *cobra.Command, args []string) error {
 	autoDiscoveryMode := len(config.Charts) == 0 && len(config.Preflights) == 0 && len(config.Manifests) == 0
 
 	if autoDiscoveryMode {
-		fmt.Fprintf(r.w, "No .replicated config found. Auto-discovering lintable resources in current directory...\n\n")
-		r.w.Flush()
+		showAutoDiscoveryMessages := r.outputFormat == "table"
+
+		if showAutoDiscoveryMessages {
+			fmt.Fprintf(r.w, "No .replicated config found. Auto-discovering lintable resources in current directory...\n\n")
+			r.w.Flush()
+		}
 
 		// Auto-discover Helm charts (for counting and display)
 		chartPaths, err := lint2.DiscoverChartPaths(filepath.Join(".", "**"))
@@ -190,18 +194,28 @@ func (r *runners) runLint(cmd *cobra.Command, args []string) error {
 		}
 
 		// Print what was discovered
-		fmt.Fprintf(r.w, "Discovered resources:\n")
-		fmt.Fprintf(r.w, "  - %d Helm chart(s)\n", len(chartPaths))
-		fmt.Fprintf(r.w, "  - %d Preflight spec(s)\n", len(preflightPaths))
-		fmt.Fprintf(r.w, "  - %d Support Bundle spec(s)\n", len(sbPaths))
-		fmt.Fprintf(r.w, "  - %d HelmChart manifest(s)\n\n", len(helmChartPaths))
-		r.w.Flush()
+		if showAutoDiscoveryMessages {
+			fmt.Fprintf(r.w, "Discovered resources:\n")
+			fmt.Fprintf(r.w, "  - %d Helm chart(s)\n", len(chartPaths))
+			fmt.Fprintf(r.w, "  - %d Preflight spec(s)\n", len(preflightPaths))
+			fmt.Fprintf(r.w, "  - %d Support Bundle spec(s)\n", len(sbPaths))
+			fmt.Fprintf(r.w, "  - %d HelmChart manifest(s)\n\n", len(helmChartPaths))
+			r.w.Flush()
+		}
 
 		// If nothing was found and EC linting is not enabled, exit early.
 		// EC linting runs after this block, so don't bail out when it's enabled.
 		if len(chartPaths) == 0 && len(preflightPaths) == 0 && len(sbPaths) == 0 && !config.ReplLint.Linters.EmbeddedCluster.IsEnabled() {
-			fmt.Fprintf(r.w, "No lintable resources found in current directory.\n")
-			r.w.Flush()
+			if showAutoDiscoveryMessages {
+				fmt.Fprintf(r.w, "No lintable resources found in current directory.\n")
+				r.w.Flush()
+			}
+			if r.outputFormat == "json" {
+				output.Summary = r.calculateOverallSummary(output)
+				if err := print.LintResults(r.outputFormat, r.w, output); err != nil {
+					return errors.Wrap(err, "failed to print JSON output to stdout")
+				}
+			}
 			return nil
 		}
 	}
diff --git a/cli/cmd/release_create.go b/cli/cmd/release_create.go
index 9c8eb2971..b167823d5 100644
--- a/cli/cmd/release_create.go
+++ b/cli/cmd/release_create.go
@@ -230,7 +230,7 @@ func (r *runners) releaseCreate(cmd *cobra.Command, args []string) (err error) {
 		printIfError(cmd, err)
 	}()
 
-	log := logger.NewLogger(r.w)
+	log := logger.NewLogger(r.w).SetIsTerminal(r.stdoutIsTTY)
 	if r.outputFormat == "json" {
 		// suppress log lines for machine-readable output
 		log.Silence()
diff --git a/cli/cmd/release_download.go b/cli/cmd/release_download.go
index 80e81cc11..a152ff807 100644
--- a/cli/cmd/release_download.go
+++ b/cli/cmd/release_download.go
@@ -105,7 +105,7 @@ func (r *runners) releaseDownload(command *cobra.Command, args []string) error {
 		return r.releaseInspect(command, args)
 	}
 
-	log := logger.NewLogger(os.Stdout)
+	log := logger.NewLogger(os.Stderr)
 
 	// Determine sequence to download
 	var seq int64
@@ -280,7 +280,7 @@ func (r *runners) downloadReleaseArchive(seq int64, dest string) error {
 	}
 	defer os.RemoveAll(tempDir)
 
-	log := logger.NewLogger(os.Stdout)
+	log := logger.NewLogger(os.Stderr)
 	if err := kotsrelease.Save(tempDir, release, log); err != nil {
 		return errors.Wrap(err, "save release to temp dir")
 	}
diff --git a/cli/cmd/root.go b/cli/cmd/root.go
index 226f41d34..866370836 100644
--- a/cli/cmd/root.go
+++ b/cli/cmd/root.go
@@ -9,6 +9,7 @@ import (
 	"text/tabwriter"
 
 	"github.com/Masterminds/sprig/v3"
+	"github.com/mattn/go-isatty"
 	"github.com/pkg/errors"
 	"github.com/replicatedhq/replicated/client"
 	replicatedcache "github.com/replicatedhq/replicated/pkg/cache"
@@ -104,20 +105,31 @@ Use "{{.CommandPath}} [command] --help" for more information about a command.{{e
 func Execute(rootCmd *cobra.Command, stdin io.Reader, stdout io.Writer, stderr io.Writer) error {
 	w := tabwriter.NewWriter(stdout, minWidth, tabWidth, padding, padChar, tabwriter.TabIndent)
 
+	stdoutIsTTY := false
+	if f, ok := stdout.(*os.File); ok {
+		stdoutIsTTY = isatty.IsTerminal(f.Fd())
+	}
+
 	// get api client and app ID after flags are parsed
 	runCmds := &runners{
-		rootCmd: rootCmd,
-		stdin:   stdin,
-		w:       w,
+		rootCmd:     rootCmd,
+		stdin:       stdin,
+		w:           w,
+		stdoutIsTTY: stdoutIsTTY,
 	}
 	if runCmds.rootCmd == nil {
 		runCmds.rootCmd = GetRootCmd()
 	}
 	if stderr != nil {
 		runCmds.rootCmd.SetErr(stderr)
+		runCmds.rootCmd.SetOut(stderr)
 	}
 	if stdout != nil {
-		runCmds.rootCmd.SetOut(stdout)
+		defaultHelpFunc := runCmds.rootCmd.HelpFunc()
+		runCmds.rootCmd.SetHelpFunc(func(cmd *cobra.Command, args []string) {
+			cmd.SetOut(stdout)
+			defaultHelpFunc(cmd, args)
+		})
 	}
 
 	// Setup PersistentPreRun to handle --debug flag
diff --git a/cli/cmd/runner.go b/cli/cmd/runner.go
index d9f376d06..1f54411a4 100644
--- a/cli/cmd/runner.go
+++ b/cli/cmd/runner.go
@@ -24,6 +24,7 @@ type runners struct {
 	stdin        io.Reader
 	outputFormat string
 	w            *tabwriter.Writer
+	stdoutIsTTY  bool
 
 	rootCmd *cobra.Command
 	args    runnerArgs
diff --git a/pkg/logger/logger.go b/pkg/logger/logger.go
index 808e258c7..f883b95ba 100644
--- a/pkg/logger/logger.go
+++ b/pkg/logger/logger.go
@@ -18,6 +18,7 @@ type Logger struct {
 	spinnerArgs   []interface{}
 	isSilent      bool
 	isVerbose     bool
+	isTerminal    *bool
 }
 
 func NewLogger(writer io.Writer) *Logger {
@@ -26,6 +27,27 @@ func NewLogger(writer io.Writer) *Logger {
 	}
 }
 
+// SetIsTerminal lets callers override TTY detection. Useful when the
+// logger writes through a wrapper (e.g. tabwriter) that hides the
+// underlying file descriptor.
+func (l *Logger) SetIsTerminal(isTerminal bool) *Logger {
+	if l == nil {
+		return l
+	}
+	l.isTerminal = &isTerminal
+	return l
+}
+
+func (l *Logger) isTTY() bool {
+	if l.isTerminal != nil {
+		return *l.isTerminal
+	}
+	if f, ok := l.w.(*os.File); ok {
+		return isatty.IsTerminal(f.Fd())
+	}
+	return false
+}
+
 func (l *Logger) Silence() {
 	if l == nil {
 		return
@@ -107,7 +129,7 @@ func (l *Logger) ActionWithSpinner(msg string, args ...interface{}) {
 	fmt.Fprintf(l.w, "  • ")
 	fmt.Fprintf(l.w, msg, args...)
 
-	if isatty.IsTerminal(os.Stdout.Fd()) {
+	if l.isTTY() {
 		s := spin.New()
 
 		fmt.Fprintf(l.w, " %s", s.Next())
@@ -140,7 +162,7 @@ func (l *Logger) ChildActionWithSpinner(msg string, args ...interface{}) {
 	fmt.Fprintf(l.w, "    • ")
 	fmt.Fprintf(l.w, msg, args...)
 
-	if isatty.IsTerminal(os.Stdout.Fd()) {
+	if l.isTTY() {
 		s := spin.New()
 
 		fmt.Fprintf(l.w, " %s", s.Next())
@@ -178,7 +200,7 @@ func (l *Logger) FinishChildSpinner() {
 	green.Fprintf(l.w, " ✓")
 	fmt.Fprintf(l.w, "  \n")
 
-	if isatty.IsTerminal(os.Stdout.Fd()) {
+	if l.isTTY() {
 		l.spinnerStopCh <- true
 		close(l.spinnerStopCh)
 	}
@@ -207,7 +229,7 @@ func (l *Logger) FinishSpinner() {
 	green.Fprintf(l.w, " ✓")
 	fmt.Fprintf(l.w, "  \n")
 
-	if isatty.IsTerminal(os.Stdout.Fd()) {
+	if l.isTTY() {
 		l.spinnerStopCh <- true
 		close(l.spinnerStopCh)
 	}
@@ -226,7 +248,7 @@ func (l *Logger) FinishSpinnerWithError() {
 	red.Fprintf(l.w, " ✗")
 	fmt.Fprintf(l.w, "  \n")
 
-	if isatty.IsTerminal(os.Stdout.Fd()) {
+	if l.isTTY() {
 		l.spinnerStopCh <- true
 		close(l.spinnerStopCh)
 	}