diff --git a/pkg/cmd/completion/completion_test.go b/pkg/cmd/completion/completion_test.go
index 954a937be..d1b595544 100644
--- a/pkg/cmd/completion/completion_test.go
+++ b/pkg/cmd/completion/completion_test.go
@@ -54,7 +54,7 @@ func TestNewCmdCompletion(t *testing.T) {
 				t.Fatalf("argument splitting error: %v", err)
 			}
 			rootCmd.SetArgs(argv)
-			rootCmd.SetOut(stdout)
+			rootCmd.SetOut(stderr)
 			rootCmd.SetErr(stderr)
 
 			_, err = rootCmd.ExecuteC()
diff --git a/pkg/cmd/gist/clone/clone_test.go b/pkg/cmd/gist/clone/clone_test.go
index 71773b0d2..ebf9b5c31 100644
--- a/pkg/cmd/gist/clone/clone_test.go
+++ b/pkg/cmd/gist/clone/clone_test.go
@@ -33,7 +33,7 @@ func runCloneCommand(httpClient *http.Client, cli string) (*test.CmdOut, error)
 	cmd.SetArgs(argv)
 
 	cmd.SetIn(stdin)
-	cmd.SetOut(stdout)
+	cmd.SetOut(stderr)
 	cmd.SetErr(stderr)
 
 	if err != nil {
diff --git a/pkg/cmd/pr/create/create_test.go b/pkg/cmd/pr/create/create_test.go
index 9f7d8ce44..33feafa40 100644
--- a/pkg/cmd/pr/create/create_test.go
+++ b/pkg/cmd/pr/create/create_test.go
@@ -155,7 +155,7 @@ func TestNewCmdCreate(t *testing.T) {
 			args, err := shlex.Split(tt.cli)
 			require.NoError(t, err)
 			cmd.SetArgs(args)
-			cmd.SetOut(stdout)
+			cmd.SetOut(stderr)
 			cmd.SetErr(stderr)
 			_, err = cmd.ExecuteC()
 			if tt.wantsErr {
diff --git a/pkg/cmd/repo/clone/clone_test.go b/pkg/cmd/repo/clone/clone_test.go
index 06c53c325..8eefd32ca 100644
--- a/pkg/cmd/repo/clone/clone_test.go
+++ b/pkg/cmd/repo/clone/clone_test.go
@@ -74,7 +74,7 @@ func TestNewCmdClone(t *testing.T) {
 			cmd.SetArgs(argv)
 
 			cmd.SetIn(stdin)
-			cmd.SetOut(stdout)
+			cmd.SetOut(stderr)
 			cmd.SetErr(stderr)
 
 			_, err = cmd.ExecuteC()
@@ -112,7 +112,7 @@ func runCloneCommand(httpClient *http.Client, cli string) (*test.CmdOut, error)
 	cmd.SetArgs(argv)
 
 	cmd.SetIn(stdin)
-	cmd.SetOut(stdout)
+	cmd.SetOut(stderr)
 	cmd.SetErr(stderr)
 
 	if err != nil {
diff --git a/pkg/cmd/root/help.go b/pkg/cmd/root/help.go
index d8b3e18b1..c7940faf0 100644
--- a/pkg/cmd/root/help.go
+++ b/pkg/cmd/root/help.go
@@ -3,6 +3,7 @@ package root
 import (
 	"bytes"
 	"fmt"
+	"io"
 	"sort"
 	"strings"
 
@@ -12,25 +13,25 @@ import (
 	"github.com/spf13/pflag"
 )
 
-func rootUsageFunc(command *cobra.Command) error {
-	command.Printf("Usage:  %s", command.UseLine())
+func rootUsageFunc(w io.Writer, command *cobra.Command) error {
+	fmt.Fprintf(w, "Usage:  %s", command.UseLine())
 
 	subcommands := command.Commands()
 	if len(subcommands) > 0 {
-		command.Print("\n\nAvailable commands:\n")
+		fmt.Fprint(w, "\n\nAvailable commands:\n")
 		for _, c := range subcommands {
 			if c.Hidden {
 				continue
 			}
-			command.Printf("  %s\n", c.Name())
+			fmt.Fprintf(w, "  %s\n", c.Name())
 		}
 		return nil
 	}
 
 	flagUsages := command.LocalFlags().FlagUsages()
 	if flagUsages != "" {
-		command.Println("\n\nFlags:")
-		command.Print(text.Indent(dedent(flagUsages), "  "))
+		fmt.Fprintln(w, "\n\nFlags:")
+		fmt.Fprint(w, text.Indent(dedent(flagUsages), "  "))
 	}
 	return nil
 }
@@ -52,8 +53,8 @@ func HasFailed() bool {
 // Display helpful error message in case subcommand name was mistyped.
 // This matches Cobra's behavior for root command, which Cobra
 // confusingly doesn't apply to nested commands.
-func nestedSuggestFunc(command *cobra.Command, arg string) {
-	command.Printf("unknown command %q for %q\n", arg, command.CommandPath())
+func nestedSuggestFunc(w io.Writer, command *cobra.Command, arg string) {
+	fmt.Fprintf(w, "unknown command %q for %q\n", arg, command.CommandPath())
 
 	var candidates []string
 	if arg == "help" {
@@ -66,14 +67,14 @@ func nestedSuggestFunc(command *cobra.Command, arg string) {
 	}
 
 	if len(candidates) > 0 {
-		command.Print("\nDid you mean this?\n")
+		fmt.Fprint(w, "\nDid you mean this?\n")
 		for _, c := range candidates {
-			command.Printf("\t%s\n", c)
+			fmt.Fprintf(w, "\t%s\n", c)
 		}
 	}
 
-	command.Print("\n")
-	_ = rootUsageFunc(command)
+	fmt.Fprint(w, "\n")
+	_ = rootUsageFunc(w, command)
 }
 
 func isRootCmd(command *cobra.Command) bool {
@@ -84,7 +85,7 @@ func rootHelpFunc(f *cmdutil.Factory, command *cobra.Command, args []string) {
 	cs := f.IOStreams.ColorScheme()
 
 	if isRootCmd(command.Parent()) && len(args) >= 2 && args[1] != "--help" && args[1] != "-h" {
-		nestedSuggestFunc(command, args[1])
+		nestedSuggestFunc(f.IOStreams.ErrOut, command, args[1])
 		hasFailed = true
 		return
 	}
@@ -190,7 +191,7 @@ Read the manual at https://cli.github.com/manual`})
 		helpEntries = append(helpEntries, helpEntry{"FEEDBACK", command.Annotations["help:feedback"]})
 	}
 
-	out := command.OutOrStdout()
+	out := f.IOStreams.Out
 	for _, e := range helpEntries {
 		if e.Title != "" {
 			// If there is a title, add indentation to each line in the body
diff --git a/pkg/cmd/root/help_topic.go b/pkg/cmd/root/help_topic.go
index 757e972ed..05798894b 100644
--- a/pkg/cmd/root/help_topic.go
+++ b/pkg/cmd/root/help_topic.go
@@ -1,7 +1,11 @@
 package root
 
 import (
+	"fmt"
+	"io"
+
 	"github.com/MakeNowJust/heredoc"
+	"github.com/cli/cli/v2/pkg/iostreams"
 	"github.com/cli/cli/v2/pkg/text"
 	"github.com/spf13/cobra"
 )
@@ -127,7 +131,7 @@ var HelpTopics = map[string]map[string]string{
 	},
 }
 
-func NewHelpTopic(topic string) *cobra.Command {
+func NewHelpTopic(ios *iostreams.IOStreams, topic string) *cobra.Command {
 	cmd := &cobra.Command{
 		Use:     topic,
 		Short:   HelpTopics[topic]["short"],
@@ -140,21 +144,25 @@ func NewHelpTopic(topic string) *cobra.Command {
 		},
 	}
 
-	cmd.SetHelpFunc(helpTopicHelpFunc)
-	cmd.SetUsageFunc(helpTopicUsageFunc)
+	cmd.SetHelpFunc(func(c *cobra.Command, args []string) {
+		helpTopicHelpFunc(ios.Out, c, args)
+	})
+	cmd.SetUsageFunc(func(c *cobra.Command) error {
+		return helpTopicUsageFunc(ios.ErrOut, c)
+	})
 
 	return cmd
 }
 
-func helpTopicHelpFunc(command *cobra.Command, args []string) {
-	command.Print(command.Long)
+func helpTopicHelpFunc(w io.Writer, command *cobra.Command, args []string) {
+	fmt.Fprint(w, command.Long)
 	if command.Example != "" {
-		command.Printf("\n\nEXAMPLES\n")
-		command.Print(text.Indent(command.Example, "  "))
+		fmt.Fprintf(w, "\n\nEXAMPLES\n")
+		fmt.Fprint(w, text.Indent(command.Example, "  "))
 	}
 }
 
-func helpTopicUsageFunc(command *cobra.Command) error {
-	command.Printf("Usage: gh help %s", command.Use)
+func helpTopicUsageFunc(w io.Writer, command *cobra.Command) error {
+	fmt.Fprintf(w, "Usage: gh help %s", command.Use)
 	return nil
 }
diff --git a/pkg/cmd/root/help_topic_test.go b/pkg/cmd/root/help_topic_test.go
index c5c51408f..5f6825912 100644
--- a/pkg/cmd/root/help_topic_test.go
+++ b/pkg/cmd/root/help_topic_test.go
@@ -61,11 +61,11 @@ func TestNewHelpTopic(t *testing.T) {
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			_, _, stdout, stderr := iostreams.Test()
+			ios, _, _, stderr := iostreams.Test()
 
-			cmd := NewHelpTopic(tt.topic)
+			cmd := NewHelpTopic(ios, tt.topic)
 			cmd.SetArgs(append(tt.args, tt.flags...))
-			cmd.SetOut(stdout)
+			cmd.SetOut(stderr)
 			cmd.SetErr(stderr)
 
 			_, err := cmd.ExecuteC()
diff --git a/pkg/cmd/root/root.go b/pkg/cmd/root/root.go
index 4c21330a5..4aa65c798 100644
--- a/pkg/cmd/root/root.go
+++ b/pkg/cmd/root/root.go
@@ -56,14 +56,16 @@ func NewCmdRoot(f *cmdutil.Factory, version, buildDate string) *cobra.Command {
 		},
 	}
 
-	cmd.SetOut(f.IOStreams.Out)
-	cmd.SetErr(f.IOStreams.ErrOut)
+	cmd.SetOut(f.IOStreams.ErrOut) // command usage summary and deprecation warnings
+	cmd.SetErr(f.IOStreams.ErrOut) // error messages
 
 	cmd.PersistentFlags().Bool("help", false, "Show help for command")
-	cmd.SetHelpFunc(func(cmd *cobra.Command, args []string) {
-		rootHelpFunc(f, cmd, args)
+	cmd.SetHelpFunc(func(c *cobra.Command, args []string) {
+		rootHelpFunc(f, c, args)
+	})
+	cmd.SetUsageFunc(func(c *cobra.Command) error {
+		return rootUsageFunc(f.IOStreams.ErrOut, c)
 	})
-	cmd.SetUsageFunc(rootUsageFunc)
 	cmd.SetFlagErrorFunc(rootFlagErrorFunc)
 
 	formattedVersion := versionCmd.Format(version, buildDate)
@@ -108,10 +110,10 @@ func NewCmdRoot(f *cmdutil.Factory, version, buildDate string) *cobra.Command {
 	cmd.AddCommand(labelCmd.NewCmdLabel(&repoResolvingCmdFactory))
 
 	// Help topics
-	cmd.AddCommand(NewHelpTopic("environment"))
-	cmd.AddCommand(NewHelpTopic("formatting"))
-	cmd.AddCommand(NewHelpTopic("mintty"))
-	referenceCmd := NewHelpTopic("reference")
+	cmd.AddCommand(NewHelpTopic(f.IOStreams, "environment"))
+	cmd.AddCommand(NewHelpTopic(f.IOStreams, "formatting"))
+	cmd.AddCommand(NewHelpTopic(f.IOStreams, "mintty"))
+	referenceCmd := NewHelpTopic(f.IOStreams, "reference")
 	referenceCmd.SetHelpFunc(referenceHelpFn(f.IOStreams))
 	cmd.AddCommand(referenceCmd)