diff --git a/cmd/cue/cmd/root.go b/cmd/cue/cmd/root.go
index 11bea7b1723..dea05c9129c 100644
--- a/cmd/cue/cmd/root.go
+++ b/cmd/cue/cmd/root.go
@@ -85,20 +85,16 @@ type Stats struct {
 	}
 }
 
-var hasRunCommand bool
-
 func mkRunE(c *Command, f runFunction) func(*cobra.Command, []string) error {
 	return func(cmd *cobra.Command, args []string) error {
-		// The init work below should only happen once per cmd/cue invocation;
-		// if it happens twice, we'll misbehave by writing stats twice
-		// or miscalculating pprof and stats numbers.
-		if hasRunCommand {
-			panic("cmd/cue/cmd.mkRunE init ran twice")
-		}
-		hasRunCommand = true
-
 		c.Command = cmd
 
+		// Note that the setup code below should only run once per cmd/cue invocation.
+		// This is because part of it modifies the global state like cueexperiment,
+		// but also because running this twice may result in broken CUE stats or Go profiles.
+		// However, users of the exposed Go API may be creating and running many commands,
+		// so we can't panic or fail if this setup work happens twice.
+
 		statsEnc, err := statsEncoder(c)
 		if err != nil {
 			return err
diff --git a/cmd/cue/cmd/root_test.go b/cmd/cue/cmd/root_test.go
index 648e55a82ce..30737858911 100644
--- a/cmd/cue/cmd/root_test.go
+++ b/cmd/cue/cmd/root_test.go
@@ -56,10 +56,7 @@ func TestCommand(t *testing.T) {
 	qt.Assert(t, qt.Equals(buf.String(), "{\n    \"foo\": 123\n}\n"))
 
 	// Verify that we can use the API exposed by the embedded cobra command.
-	// TODO(mvdan): panics due to https://cuelang.org/issue/3458; fix it.
-	qt.Assert(t, qt.PanicMatches(func() {
-		c, err = cmd.New([]string{"fmt", "nosuchfile.cue"})
-		err = c.Execute()
-		qt.Assert(t, qt.IsNotNil(err))
-	}, "cmd/cue/cmd.mkRunE init ran twice"))
+	c, err = cmd.New([]string{"fmt", "nosuchfile.cue"})
+	err = c.Execute()
+	qt.Assert(t, qt.IsNotNil(err))
 }