diff --git a/src/cmd/common/setup.go b/src/cmd/common/setup.go
index 6fab6e134b..602c6228a5 100644
--- a/src/cmd/common/setup.go
+++ b/src/cmd/common/setup.go
@@ -5,43 +5,38 @@
 package common
 
 import (
+	"errors"
 	"fmt"
 	"io"
 	"os"
 	"time"
 
-	"github.com/defenseunicorns/zarf/src/config"
-	"github.com/defenseunicorns/zarf/src/config/lang"
-	"github.com/defenseunicorns/zarf/src/pkg/message"
 	"github.com/pterm/pterm"
-)
 
-// LogLevelCLI holds the log level as input from a command
-var LogLevelCLI string
+	"github.com/defenseunicorns/zarf/src/pkg/message"
+)
 
 // SetupCLI sets up the CLI logging, interrupt functions, and more
-func SetupCLI() {
-	match := map[string]message.LogLevel{
-		"warn":  message.WarnLevel,
-		"info":  message.InfoLevel,
-		"debug": message.DebugLevel,
-		"trace": message.TraceLevel,
-	}
-
-	if config.NoColor {
+func SetupCLI(logLevel string, skipLogFile, noColor bool) error {
+	if noColor {
 		message.DisableColor()
 	}
 
 	printViperConfigUsed()
 
-	// No log level set, so use the default
-	if LogLevelCLI != "" {
-		if lvl, ok := match[LogLevelCLI]; ok {
-			message.SetLogLevel(lvl)
-			message.Debug("Log level set to " + LogLevelCLI)
-		} else {
-			message.Warn(lang.RootCmdErrInvalidLogLevel)
+	if logLevel != "" {
+		match := map[string]message.LogLevel{
+			"warn":  message.WarnLevel,
+			"info":  message.InfoLevel,
+			"debug": message.DebugLevel,
+			"trace": message.TraceLevel,
+		}
+		lvl, ok := match[logLevel]
+		if !ok {
+			return errors.New("invalid log level, valid options are warn, info, debug, and trace")
 		}
+		message.SetLogLevel(lvl)
+		message.Debug("Log level set to " + logLevel)
 	}
 
 	// Disable progress bars for CI envs
@@ -50,21 +45,18 @@ func SetupCLI() {
 		message.NoProgress = true
 	}
 
-	if !config.SkipLogFile {
+	if !skipLogFile {
 		ts := time.Now().Format("2006-01-02-15-04-05")
-
 		f, err := os.CreateTemp("", fmt.Sprintf("zarf-%s-*.log", ts))
 		if err != nil {
-			message.WarnErr(err, "Error creating a log file in a temporary directory")
-			return
+			return fmt.Errorf("could not create a log file in a the temporary directory: %w", err)
 		}
 		logFile, err := message.UseLogFile(f)
 		if err != nil {
-			message.WarnErr(err, "Error saving a log file to a temporary directory")
-			return
+			return fmt.Errorf("could not save a log file to the temporary directory: %w", err)
 		}
-
 		pterm.SetDefaultOutput(io.MultiWriter(os.Stderr, logFile))
 		message.Notef("Saving log file to %s", f.Name())
 	}
+	return nil
 }
diff --git a/src/cmd/root.go b/src/cmd/root.go
index ee40254fe0..b8d68028ed 100644
--- a/src/cmd/root.go
+++ b/src/cmd/root.go
@@ -26,20 +26,40 @@ import (
 var (
 	// Default global config for the packager
 	pkgConfig = types.PackagerConfig{}
+	// LogLevelCLI holds the log level as input from a command
+	LogLevelCLI string
+	// SkipLogFile is a flag to skip logging to a file
+	SkipLogFile bool
+	// NoColor is a flag to disable colors in output
+	NoColor bool
 )
 
 var rootCmd = &cobra.Command{
 	Use: "zarf COMMAND",
-	PersistentPreRun: func(cmd *cobra.Command, _ []string) {
+	PersistentPreRunE: func(cmd *cobra.Command, _ []string) error {
 		// Skip for vendor-only commands
 		if common.CheckVendorOnlyFromPath(cmd) {
-			return
+			return nil
 		}
-		// Don't log the help command
+
+		skipLogFile := SkipLogFile
+
+		// Dont write tool commands to file.
+		comps := strings.Split(cmd.CommandPath(), " ")
+		if len(comps) > 1 && comps[1] == "tools" {
+			skipLogFile = true
+		}
+
+		// Dont write help command to file.
 		if cmd.Parent() == nil {
-			config.SkipLogFile = true
+			skipLogFile = true
+		}
+
+		err := common.SetupCLI(LogLevelCLI, skipLogFile, NoColor)
+		if err != nil {
+			return err
 		}
-		common.SetupCLI()
+		return nil
 	},
 	Short:         lang.RootCmdShort,
 	Long:          lang.RootCmdLong,
@@ -89,11 +109,11 @@ func init() {
 
 	v := common.InitViper()
 
-	rootCmd.PersistentFlags().StringVarP(&common.LogLevelCLI, "log-level", "l", v.GetString(common.VLogLevel), lang.RootCmdFlagLogLevel)
+	rootCmd.PersistentFlags().StringVarP(&LogLevelCLI, "log-level", "l", v.GetString(common.VLogLevel), lang.RootCmdFlagLogLevel)
 	rootCmd.PersistentFlags().StringVarP(&config.CLIArch, "architecture", "a", v.GetString(common.VArchitecture), lang.RootCmdFlagArch)
-	rootCmd.PersistentFlags().BoolVar(&config.SkipLogFile, "no-log-file", v.GetBool(common.VNoLogFile), lang.RootCmdFlagSkipLogFile)
+	rootCmd.PersistentFlags().BoolVar(&SkipLogFile, "no-log-file", v.GetBool(common.VNoLogFile), lang.RootCmdFlagSkipLogFile)
 	rootCmd.PersistentFlags().BoolVar(&message.NoProgress, "no-progress", v.GetBool(common.VNoProgress), lang.RootCmdFlagNoProgress)
-	rootCmd.PersistentFlags().BoolVar(&config.NoColor, "no-color", v.GetBool(common.VNoColor), lang.RootCmdFlagNoColor)
+	rootCmd.PersistentFlags().BoolVar(&NoColor, "no-color", v.GetBool(common.VNoColor), lang.RootCmdFlagNoColor)
 	rootCmd.PersistentFlags().StringVar(&config.CommonOptions.CachePath, "zarf-cache", v.GetString(common.VZarfCache), lang.RootCmdFlagCachePath)
 	rootCmd.PersistentFlags().StringVar(&config.CommonOptions.TempDirectory, "tmpdir", v.GetString(common.VTmpDir), lang.RootCmdFlagTempDir)
 	rootCmd.PersistentFlags().BoolVar(&config.CommonOptions.Insecure, "insecure", v.GetBool(common.VInsecure), lang.RootCmdFlagInsecure)
diff --git a/src/cmd/tools/common.go b/src/cmd/tools/common.go
index 0844df9801..015d766d69 100644
--- a/src/cmd/tools/common.go
+++ b/src/cmd/tools/common.go
@@ -7,26 +7,15 @@ package tools
 import (
 	"fmt"
 
-	"github.com/defenseunicorns/zarf/src/cmd/common"
-	"github.com/defenseunicorns/zarf/src/config"
-	"github.com/defenseunicorns/zarf/src/config/lang"
 	"github.com/spf13/cobra"
+
+	"github.com/defenseunicorns/zarf/src/config/lang"
 )
 
 var toolsCmd = &cobra.Command{
 	Use:     "tools",
 	Aliases: []string{"t"},
-	PersistentPreRun: func(cmd *cobra.Command, _ []string) {
-		config.SkipLogFile = true
-
-		// Skip for vendor-only commands
-		if common.CheckVendorOnlyFromPath(cmd) {
-			return
-		}
-
-		common.SetupCLI()
-	},
-	Short: lang.CmdToolsShort,
+	Short:   lang.CmdToolsShort,
 }
 
 // Include adds the tools command to the root command.
diff --git a/src/cmd/version.go b/src/cmd/version.go
index 589cab9929..4c5ae94bdc 100644
--- a/src/cmd/version.go
+++ b/src/cmd/version.go
@@ -24,11 +24,8 @@ var outputFormat string
 var versionCmd = &cobra.Command{
 	Use:     "version",
 	Aliases: []string{"v"},
-	PersistentPreRun: func(_ *cobra.Command, _ []string) {
-		config.SkipLogFile = true
-	},
-	Short: lang.CmdVersionShort,
-	Long:  lang.CmdVersionLong,
+	Short:   lang.CmdVersionShort,
+	Long:    lang.CmdVersionLong,
 	RunE: func(_ *cobra.Command, _ []string) error {
 		if outputFormat == "" {
 			fmt.Println(config.CLIVersion)
diff --git a/src/config/config.go b/src/config/config.go
index f9dfc580ab..0c650419cc 100644
--- a/src/config/config.go
+++ b/src/config/config.go
@@ -60,12 +60,6 @@ var (
 	// ZarfSeedPort is the NodePort Zarf uses for the 'seed registry'
 	ZarfSeedPort string
 
-	// SkipLogFile is a flag to skip logging to a file
-	SkipLogFile bool
-
-	// NoColor is a flag to disable colors in output
-	NoColor bool
-
 	CosignPublicKey string
 
 	// Timestamp of when the CLI was started
diff --git a/src/config/lang/english.go b/src/config/lang/english.go
index df39428f48..9b90c23b22 100644
--- a/src/config/lang/english.go
+++ b/src/config/lang/english.go
@@ -58,8 +58,6 @@ const (
 	RootCmdDeprecatedDeploy = "Deprecated: Please use \"zarf package deploy %s\" to deploy this package.  This warning will be removed in Zarf v1.0.0."
 	RootCmdDeprecatedCreate = "Deprecated: Please use \"zarf package create\" to create this package.  This warning will be removed in Zarf v1.0.0."
 
-	RootCmdErrInvalidLogLevel = "Invalid log level. Valid options are: warn, info, debug, trace."
-
 	// zarf connect
 	CmdConnectShort = "Accesses services or pods deployed in the cluster"
 	CmdConnectLong  = "Uses a k8s port-forward to connect to resources within the cluster referenced by your kube-context.\n" +
diff --git a/src/pkg/message/message.go b/src/pkg/message/message.go
index 0ead8b0e01..e271cbf9d4 100644
--- a/src/pkg/message/message.go
+++ b/src/pkg/message/message.go
@@ -12,7 +12,6 @@ import (
 	"time"
 
 	"github.com/defenseunicorns/pkg/helpers/v2"
-	"github.com/defenseunicorns/zarf/src/config"
 	"github.com/fatih/color"
 	"github.com/pterm/pterm"
 )
@@ -99,6 +98,11 @@ func DisableColor() {
 	pterm.DisableColor()
 }
 
+// ColorEnabled returns true if color printing is enabled.
+func ColorEnabled() bool {
+	return pterm.PrintColor
+}
+
 // ZarfCommand prints a zarf terminal command.
 func ZarfCommand(format string, a ...any) {
 	Command("zarf "+format, a...)
@@ -276,7 +280,7 @@ func Table(header []string, data [][]string) {
 // preventing future characters from taking on the given color
 // returns string as normal if color is disabled
 func ColorWrap(str string, attr color.Attribute) string {
-	if config.NoColor || str == "" {
+	if !ColorEnabled() || str == "" {
 		return str
 	}
 	return fmt.Sprintf("\x1b[%dm%s\x1b[0m", attr, str)
diff --git a/src/pkg/utils/yaml.go b/src/pkg/utils/yaml.go
index bc49d46502..1d33c4dc4e 100644
--- a/src/pkg/utils/yaml.go
+++ b/src/pkg/utils/yaml.go
@@ -15,7 +15,6 @@ import (
 	"regexp"
 	"strings"
 
-	"github.com/defenseunicorns/zarf/src/config"
 	"github.com/defenseunicorns/zarf/src/pkg/message"
 	"github.com/fatih/color"
 	goyaml "github.com/goccy/go-yaml"
@@ -93,7 +92,7 @@ func ColorPrintYAML(data any, hints map[string]string, spaceRootLists bool) {
 		outputYAML = strings.Replace(outputYAML, key, value, 1)
 	}
 
-	if config.NoColor {
+	if !message.ColorEnabled() {
 		// If no color is specified strip any color codes from the output - https://regex101.com/r/YFyIwC/2
 		ansiRegex := regexp.MustCompile(`\x1b\[(.*?)m`)
 		outputYAML = ansiRegex.ReplaceAllString(outputYAML, "")