diff --git a/cmd/d2/help.go b/cmd/d2/help.go
index 961c9c275..3e18a56cf 100644
--- a/cmd/d2/help.go
+++ b/cmd/d2/help.go
@@ -28,13 +28,13 @@ Subcommands:
   %[1]s layout [layout name] - Display long help for a particular layout engine
 
 See more docs and the source code at https://oss.terrastruct.com/d2
-`, ms.Name, ms.FlagHelp())
+`, ms.Name, ms.Opts.Help())
 }
 
 func layoutHelp(ctx context.Context, ms *xmain.State) error {
-	if len(ms.FlagSet.Args()) == 1 {
+	if len(ms.Opts.Args()) == 1 {
 		return shortLayoutHelp(ctx, ms)
-	} else if len(ms.FlagSet.Args()) == 2 {
+	} else if len(ms.Opts.Args()) == 2 {
 		return longLayoutHelp(ctx, ms)
 	} else {
 		return pluginSubcommand(ctx, ms)
@@ -61,7 +61,7 @@ func shortLayoutHelp(ctx context.Context, ms *xmain.State) error {
 %s
 
 Usage:
-  To use a particular layout engine, set the environment variable D2_LAYOUT=[layout name].
+  To use a particular layout engine, set the environment variable D2_LAYOUT=[name] or flag --layout=[name].
 
 Example:
   D2_LAYOUT=dagre d2 in.d2 out.svg
@@ -75,7 +75,7 @@ See more docs at https://oss.terrastruct.com/d2
 }
 
 func longLayoutHelp(ctx context.Context, ms *xmain.State) error {
-	layout := ms.FlagSet.Arg(1)
+	layout := ms.Opts.Arg(1)
 	plugin, path, err := d2plugin.FindPlugin(ctx, layout)
 	if errors.Is(err, exec.ErrNotFound) {
 		return layoutNotFound(ctx, layout)
@@ -119,13 +119,13 @@ For more information on setup, please visit https://github.com/terrastruct/d2.`,
 }
 
 func pluginSubcommand(ctx context.Context, ms *xmain.State) error {
-	layout := ms.FlagSet.Arg(1)
+	layout := ms.Opts.Arg(1)
 	plugin, _, err := d2plugin.FindPlugin(ctx, layout)
 	if errors.Is(err, exec.ErrNotFound) {
 		return layoutNotFound(ctx, layout)
 	}
 
-	ms.Args = ms.FlagSet.Args()[2:]
+	ms.Opts.SetArgs(ms.Opts.Args()[2:])
 	return d2plugin.Serve(plugin)(ctx, ms)
 }
 
diff --git a/cmd/d2/main.go b/cmd/d2/main.go
index 6ce4d5459..d2f1ecdfd 100644
--- a/cmd/d2/main.go
+++ b/cmd/d2/main.go
@@ -6,7 +6,6 @@ import (
 	"fmt"
 	"os/exec"
 	"path/filepath"
-	"strconv"
 	"strings"
 	"time"
 
@@ -32,19 +31,20 @@ func run(ctx context.Context, ms *xmain.State) (err error) {
 	// :(
 	ctx = xmain.DiscardSlog(ctx)
 
-	watchFlag := ms.FlagSet.BoolP("watch", "w", false, "watch for changes to input and live reload. Use $PORT and $HOST to specify the listening address.\n$D2_PORT and $D2_HOST are also accepted and take priority. Default is localhost:0")
-	themeFlag := ms.FlagSet.Int64P("theme", "t", 0, "set the diagram theme. For a list of available options, see https://oss.terrastruct.com/d2")
-	bundleFlag := ms.FlagSet.BoolP("bundle", "b", true, "bundle all assets and layers into the output svg")
-	versionFlag := ms.FlagSet.BoolP("version", "v", false, "get the version and check for updates")
-	debugFlag := ms.FlagSet.BoolP("debug", "d", false, "print debug logs")
-	err = ms.FlagSet.Parse(ms.Args)
+	watchFlag := ms.Opts.Bool("D2_WATCH", "watch", "w", false, "watch for changes to input and live reload. Use $HOST and $PORT to specify the listening address.\n$D2_HOST and $D2_PORT are also accepted and take priority (default localhost:0, which is will open on a randomly available local port).")
+	bundleFlag := ms.Opts.Bool("D2_BUNDLE", "bundle", "b", true, "bundle all assets and layers into the output svg.")
+	debugFlag := ms.Opts.Bool("DEBUG", "debug", "d", false, "print debug logs.")
+	layoutFlag := ms.Opts.String("D2_LAYOUT", "layout", "l", "dagre", `the layout engine used.`)
+	themeFlag := ms.Opts.Int64("D2_THEME", "theme", "t", 0, "the diagram theme ID. For a list of available options, see https://oss.terrastruct.com/d2")
+	versionFlag := ms.Opts.Bool("", "version", "v", false, "get the version and check for updates")
 
+	err = ms.Opts.Parse()
 	if !errors.Is(err, pflag.ErrHelp) && err != nil {
 		return xmain.UsageErrorf("failed to parse flags: %v", err)
 	}
 
-	if len(ms.FlagSet.Args()) > 0 {
-		switch ms.FlagSet.Arg(0) {
+	if len(ms.Opts.Args()) > 0 {
+		switch ms.Opts.Arg(0) {
 		case "layout":
 			return layoutHelp(ctx, ms)
 		}
@@ -62,25 +62,25 @@ func run(ctx context.Context, ms *xmain.State) (err error) {
 	var inputPath string
 	var outputPath string
 
-	if len(ms.FlagSet.Args()) == 0 {
+	if len(ms.Opts.Args()) == 0 {
 		if versionFlag != nil && *versionFlag {
 			version.CheckVersion(ctx, ms.Log)
 			return nil
 		}
 		help(ms)
 		return nil
-	} else if len(ms.FlagSet.Args()) >= 3 {
+	} else if len(ms.Opts.Args()) >= 3 {
 		return xmain.UsageErrorf("too many arguments passed")
 	}
-	if len(ms.FlagSet.Args()) >= 1 {
-		if ms.FlagSet.Arg(0) == "version" {
+	if len(ms.Opts.Args()) >= 1 {
+		if ms.Opts.Arg(0) == "version" {
 			version.CheckVersion(ctx, ms.Log)
 			return nil
 		}
-		inputPath = ms.FlagSet.Arg(0)
+		inputPath = ms.Opts.Arg(0)
 	}
-	if len(ms.FlagSet.Args()) >= 2 {
-		outputPath = ms.FlagSet.Arg(1)
+	if len(ms.Opts.Args()) >= 2 {
+		outputPath = ms.Opts.Arg(1)
 	} else {
 		if inputPath == "-" {
 			outputPath = "-"
@@ -93,16 +93,11 @@ func run(ctx context.Context, ms *xmain.State) (err error) {
 	if match == (d2themes.Theme{}) {
 		return xmain.UsageErrorf("-t[heme] could not be found. The available options are:\n%s\nYou provided: %d", d2themescatalog.CLIString(), *themeFlag)
 	}
-	ms.Env.Setenv("D2_THEME", fmt.Sprintf("%d", *themeFlag))
+	ms.Log.Debug.Printf("using theme %s (ID: %d)", match.Name, *themeFlag)
 
-	envD2Layout := ms.Env.Getenv("D2_LAYOUT")
-	if envD2Layout == "" {
-		envD2Layout = "dagre"
-	}
-
-	plugin, path, err := d2plugin.FindPlugin(ctx, envD2Layout)
+	plugin, path, err := d2plugin.FindPlugin(ctx, *layoutFlag)
 	if errors.Is(err, exec.ErrNotFound) {
-		return layoutNotFound(ctx, envD2Layout)
+		return layoutNotFound(ctx, *layoutFlag)
 	} else if err != nil {
 		return err
 	}
@@ -111,14 +106,14 @@ func run(ctx context.Context, ms *xmain.State) (err error) {
 	if path != "" {
 		pluginLocation = fmt.Sprintf("executable plugin at %s", humanPath(path))
 	}
-	ms.Log.Debug.Printf("using layout plugin %s (%s)", envD2Layout, pluginLocation)
+	ms.Log.Debug.Printf("using layout plugin %s (%s)", *layoutFlag, pluginLocation)
 
 	if *watchFlag {
 		if inputPath == "-" {
 			return xmain.UsageErrorf("-w[atch] cannot be combined with reading input from stdin")
 		}
 		ms.Env.Setenv("LOG_TIMESTAMPS", "1")
-		w, err := newWatcher(ctx, ms, plugin, inputPath, outputPath)
+		w, err := newWatcher(ctx, ms, plugin, *themeFlag, inputPath, outputPath)
 		if err != nil {
 			return err
 		}
@@ -132,7 +127,7 @@ func run(ctx context.Context, ms *xmain.State) (err error) {
 		_ = 343
 	}
 
-	_, err = compile(ctx, ms, plugin, inputPath, outputPath)
+	_, err = compile(ctx, ms, plugin, *themeFlag, inputPath, outputPath)
 	if err != nil {
 		return err
 	}
@@ -140,7 +135,7 @@ func run(ctx context.Context, ms *xmain.State) (err error) {
 	return nil
 }
 
-func compile(ctx context.Context, ms *xmain.State, plugin d2plugin.Plugin, inputPath, outputPath string) ([]byte, error) {
+func compile(ctx context.Context, ms *xmain.State, plugin d2plugin.Plugin, themeID int64, inputPath, outputPath string) ([]byte, error) {
 	input, err := ms.ReadPath(inputPath)
 	if err != nil {
 		return nil, err
@@ -151,7 +146,6 @@ func compile(ctx context.Context, ms *xmain.State, plugin d2plugin.Plugin, input
 		return nil, err
 	}
 
-	themeID, _ := strconv.ParseInt(ms.Env.Getenv("D2_THEME"), 10, 64)
 	d, err := d2.Compile(ctx, string(input), &d2.CompileOptions{
 		Layout:  plugin.Layout,
 		Ruler:   ruler,
diff --git a/cmd/d2/watch.go b/cmd/d2/watch.go
index f9570da66..18dd9ea3c 100644
--- a/cmd/d2/watch.go
+++ b/cmd/d2/watch.go
@@ -42,6 +42,7 @@ type watcher struct {
 
 	ms           *xmain.State
 	layoutPlugin d2plugin.Plugin
+	themeID      int64
 	inputPath    string
 	outputPath   string
 
@@ -68,7 +69,7 @@ type compileResult struct {
 	SVG string `json:"svg"`
 }
 
-func newWatcher(ctx context.Context, ms *xmain.State, layoutPlugin d2plugin.Plugin, inputPath, outputPath string) (*watcher, error) {
+func newWatcher(ctx context.Context, ms *xmain.State, layoutPlugin d2plugin.Plugin, themeID int64, inputPath, outputPath string) (*watcher, error) {
 	ctx, cancel := context.WithCancel(ctx)
 
 	w := &watcher{
@@ -78,6 +79,7 @@ func newWatcher(ctx context.Context, ms *xmain.State, layoutPlugin d2plugin.Plug
 
 		ms:           ms,
 		layoutPlugin: layoutPlugin,
+		themeID:      themeID,
 		inputPath:    inputPath,
 		outputPath:   outputPath,
 
@@ -325,7 +327,7 @@ func (w *watcher) compileLoop(ctx context.Context) error {
 			recompiledPrefix = "re"
 		}
 
-		b, err := compile(ctx, w.ms, w.layoutPlugin, w.inputPath, w.outputPath)
+		b, err := compile(ctx, w.ms, w.layoutPlugin, w.themeID, w.inputPath, w.outputPath)
 		if err != nil {
 			err = fmt.Errorf("failed to %scompile: %w", recompiledPrefix, err)
 			w.ms.Log.Error.Print(err)
diff --git a/d2plugin/serve.go b/d2plugin/serve.go
index 919eab48b..a51c48614 100644
--- a/d2plugin/serve.go
+++ b/d2plugin/serve.go
@@ -19,12 +19,12 @@ import (
 // Also see execPlugin in exec.go for the d2 binary plugin protocol.
 func Serve(p Plugin) func(context.Context, *xmain.State) error {
 	return func(ctx context.Context, ms *xmain.State) (err error) {
-		if len(ms.Args) < 1 {
+		if len(ms.Opts.Args()) < 1 {
 			return errors.New("expected first argument to plugin binary to be function name")
 		}
-		reqFunc := ms.Args[0]
+		reqFunc := ms.Opts.Arg(0)
 
-		switch ms.Args[0] {
+		switch ms.Opts.Arg(0) {
 		case "info":
 			return info(ctx, p, ms)
 		case "layout":
diff --git a/lib/xmain/opts.go b/lib/xmain/opts.go
new file mode 100644
index 000000000..c095d58cb
--- /dev/null
+++ b/lib/xmain/opts.go
@@ -0,0 +1,132 @@
+package xmain
+
+import (
+	"fmt"
+	"io"
+	"strconv"
+	"strings"
+
+	"github.com/spf13/pflag"
+	"oss.terrastruct.com/cmdlog"
+	"oss.terrastruct.com/xos"
+)
+
+type Opts struct {
+	args  []string
+	flags *pflag.FlagSet
+	env   *xos.Env
+	log   *cmdlog.Logger
+
+	registeredEnvs []string
+}
+
+func NewOpts(env *xos.Env, args []string, log *cmdlog.Logger) *Opts {
+	flags := pflag.NewFlagSet("", pflag.ContinueOnError)
+	flags.SortFlags = false
+	flags.Usage = func() {}
+	flags.SetOutput(io.Discard)
+	return &Opts{
+		args:  args,
+		flags: flags,
+		env:   env,
+		log:   log,
+	}
+}
+
+func (o *Opts) Help() string {
+	b := &strings.Builder{}
+	o.flags.SetOutput(b)
+	o.flags.PrintDefaults()
+
+	if len(o.registeredEnvs) > 0 {
+		b.WriteString("\nYou may persistently set the following as environment variables (flags take precedent):\n")
+		for i, e := range o.registeredEnvs {
+			s := fmt.Sprintf("- $%s", e)
+			if i != len(o.registeredEnvs)-1 {
+				s += "\n"
+			}
+			b.WriteString(s)
+		}
+	}
+
+	return b.String()
+}
+
+func (o *Opts) Int64(envKey, flag, shortFlag string, defaultVal int64, usage string) *int64 {
+	if envKey != "" {
+		if o.env.Getenv(envKey) != "" {
+			envVal, err := strconv.ParseInt(o.env.Getenv(envKey), 10, 64)
+			if err != nil {
+				o.log.Error.Printf(`ignoring invalid environment variable %s. Expected int64. Found "%v".`, envKey, envVal)
+			} else if envVal != defaultVal {
+				defaultVal = envVal
+			}
+		}
+		o.registeredEnvs = append(o.registeredEnvs, envKey)
+	}
+
+	return o.flags.Int64P(flag, shortFlag, defaultVal, usage)
+}
+
+func (o *Opts) String(envKey, flag, shortFlag string, defaultVal, usage string) *string {
+	if envKey != "" {
+		if o.env.Getenv(envKey) != "" {
+			envVal := o.env.Getenv(envKey)
+			if envVal != defaultVal {
+				defaultVal = envVal
+			}
+		}
+		o.registeredEnvs = append(o.registeredEnvs, envKey)
+	}
+
+	return o.flags.StringP(flag, shortFlag, defaultVal, usage)
+}
+
+func (o *Opts) Bool(envKey, flag, shortFlag string, defaultVal bool, usage string) *bool {
+	if envKey != "" {
+		if o.env.Getenv(envKey) != "" {
+			envVal := o.env.Getenv(envKey)
+			if !boolyEnv(envVal) {
+				o.log.Error.Printf(`ignoring invalid environment variable %s. Expected bool. Found "%s".`, envKey, envVal)
+			} else if (defaultVal && falseyEnv(envVal)) ||
+				(!defaultVal && truthyEnv(envVal)) {
+				defaultVal = !defaultVal
+			}
+		}
+		o.registeredEnvs = append(o.registeredEnvs, envKey)
+	}
+
+	return o.flags.BoolP(flag, shortFlag, defaultVal, usage)
+}
+
+func boolyEnv(s string) bool {
+	return falseyEnv(s) || truthyEnv(s)
+}
+
+func falseyEnv(s string) bool {
+	return s == "0" || s == "false" || s == "f"
+}
+
+func truthyEnv(s string) bool {
+	return s == "1" || s == "true" || s == "t"
+}
+
+func (o *Opts) Parse() error {
+	err := o.flags.Parse(o.args)
+	if err != nil {
+		return err
+	}
+	return nil
+}
+
+func (o *Opts) SetArgs(args []string) {
+	o.args = args
+}
+
+func (o *Opts) Args() []string {
+	return o.flags.Args()
+}
+
+func (o *Opts) Arg(i int) string {
+	return o.flags.Arg(i)
+}
diff --git a/lib/xmain/xmain.go b/lib/xmain/xmain.go
index d71147776..3ef9b89aa 100644
--- a/lib/xmain/xmain.go
+++ b/lib/xmain/xmain.go
@@ -9,13 +9,11 @@ import (
 	"io"
 	"os"
 	"os/signal"
-	"strings"
 	"syscall"
 	"time"
 
 	"cdr.dev/slog"
 	"cdr.dev/slog/sloggers/sloghuman"
-	"github.com/spf13/pflag"
 
 	"oss.terrastruct.com/xos"
 
@@ -41,14 +39,10 @@ func Main(run RunFunc) {
 		Stdout: os.Stdout,
 		Stderr: os.Stderr,
 
-		Env:     xos.NewEnv(os.Environ()),
-		FlagSet: pflag.NewFlagSet("", pflag.ContinueOnError),
-		Args:    args,
+		Env: xos.NewEnv(os.Environ()),
 	}
 	ms.Log = cmdlog.Log(ms.Env, os.Stderr)
-	ms.FlagSet.SortFlags = false
-	ms.FlagSet.Usage = func() {}
-	ms.FlagSet.SetOutput(io.Discard)
+	ms.Opts = NewOpts(ms.Env, args, ms.Log)
 
 	sigs := make(chan os.Signal, 1)
 	signal.Notify(sigs, os.Interrupt, syscall.SIGTERM)
@@ -88,10 +82,9 @@ type State struct {
 	Stdout io.WriteCloser
 	Stderr io.WriteCloser
 
-	Log     *cmdlog.Logger
-	Env     *xos.Env
-	Args    []string
-	FlagSet *pflag.FlagSet
+	Log  *cmdlog.Logger
+	Env  *xos.Env
+	Opts *Opts
 }
 
 func (ms *State) Main(ctx context.Context, sigs <-chan os.Signal, run func(context.Context, *State) error) error {
@@ -129,13 +122,6 @@ func (ms *State) Main(ctx context.Context, sigs <-chan os.Signal, run func(conte
 	}
 }
 
-func (ms *State) FlagHelp() string {
-	b := &strings.Builder{}
-	ms.FlagSet.SetOutput(b)
-	ms.FlagSet.PrintDefaults()
-	return b.String()
-}
-
 type ExitError struct {
 	Code    int    `json:"code"`
 	Message string `json:"message"`