diff --git a/graph-explorer/cmd/graph-explorer/main.go b/graph-explorer/cmd/graph-explorer/main.go
index f0d3cdcac7..a8357cb1f2 100644
--- a/graph-explorer/cmd/graph-explorer/main.go
+++ b/graph-explorer/cmd/graph-explorer/main.go
@@ -8,7 +8,7 @@ import (
 )
 
 func main() {
-	if err := command.Execute(config.New()); err != nil {
+	if err := command.Execute(config.DefaultConfig()); err != nil {
 		os.Exit(1)
 	}
 }
diff --git a/graph-explorer/pkg/command/root.go b/graph-explorer/pkg/command/root.go
index 6b3dd841b8..3ebaa4422f 100644
--- a/graph-explorer/pkg/command/root.go
+++ b/graph-explorer/pkg/command/root.go
@@ -3,14 +3,11 @@ package command
 import (
 	"context"
 	"os"
-	"strings"
 
 	"github.com/owncloud/ocis/graph-explorer/pkg/config"
 	ociscfg "github.com/owncloud/ocis/ocis-pkg/config"
 	"github.com/owncloud/ocis/ocis-pkg/log"
-	"github.com/owncloud/ocis/ocis-pkg/sync"
 	"github.com/owncloud/ocis/ocis-pkg/version"
-	"github.com/spf13/viper"
 	"github.com/thejerf/suture/v4"
 	"github.com/urfave/cli/v2"
 )
@@ -29,9 +26,6 @@ func Execute(cfg *config.Config) error {
 				Email: "support@owncloud.com",
 			},
 		},
-
-		//Flags: flagset.RootWithConfig(cfg),
-
 		Before: func(c *cli.Context) error {
 			cfg.Server.Version = version.String
 			return ParseConfig(c, cfg)
@@ -67,46 +61,18 @@ func NewLogger(cfg *config.Config) log.Logger {
 	)
 }
 
-// ParseConfig loads accounts configuration from Viper known paths.
+// ParseConfig loads graph configuration from known paths.
 func ParseConfig(c *cli.Context, cfg *config.Config) error {
-	sync.ParsingViperConfig.Lock()
-	defer sync.ParsingViperConfig.Unlock()
-	logger := NewLogger(cfg)
-
-	viper.SetEnvKeyReplacer(strings.NewReplacer(".", "_"))
-	viper.SetEnvPrefix("GRAPH_EXPLORER")
-	viper.AutomaticEnv()
-
-	if c.IsSet("config-file") {
-		viper.SetConfigFile(c.String("config-file"))
-	} else {
-		viper.SetConfigName("graph-explorer")
-
-		viper.AddConfigPath("/etc/ocis")
-		viper.AddConfigPath("$HOME/.ocis")
-		viper.AddConfigPath("./config")
+	conf, err := ociscfg.BindSourcesToStructs("graph-explorer", cfg)
+	if err != nil {
+		return err
 	}
 
-	if err := viper.ReadInConfig(); err != nil {
-		switch err.(type) {
-		case viper.ConfigFileNotFoundError:
-			//logger.Info().
-			//	Msg("Continue without config")
-		case viper.UnsupportedConfigError:
-			logger.Fatal().
-				Err(err).
-				Msg("Unsupported config type")
-		default:
-			logger.Fatal().
-				Err(err).
-				Msg("Failed to read config")
-		}
-	}
+	// load all env variables relevant to the config in the current context.
+	conf.LoadOSEnv(config.GetEnv(), false)
 
-	if err := viper.Unmarshal(&cfg); err != nil {
-		logger.Fatal().
-			Err(err).
-			Msg("Failed to parse config")
+	if err = cfg.UnmapEnv(conf); err != nil {
+		return err
 	}
 
 	return nil
diff --git a/graph-explorer/pkg/command/server.go b/graph-explorer/pkg/command/server.go
index fa15eaf360..773a8b61f0 100644
--- a/graph-explorer/pkg/command/server.go
+++ b/graph-explorer/pkg/command/server.go
@@ -6,7 +6,6 @@ import (
 
 	"github.com/oklog/run"
 	"github.com/owncloud/ocis/graph-explorer/pkg/config"
-	"github.com/owncloud/ocis/graph-explorer/pkg/flagset"
 	"github.com/owncloud/ocis/graph-explorer/pkg/metrics"
 	"github.com/owncloud/ocis/graph-explorer/pkg/server/debug"
 	"github.com/owncloud/ocis/graph-explorer/pkg/server/http"
@@ -20,19 +19,15 @@ func Server(cfg *config.Config) *cli.Command {
 	return &cli.Command{
 		Name:  "server",
 		Usage: "Start integrated server",
-		Flags: flagset.ServerWithConfig(cfg),
 		Before: func(ctx *cli.Context) error {
-			logger := NewLogger(cfg)
 			if cfg.HTTP.Root != "/" {
 				cfg.HTTP.Root = strings.TrimSuffix(cfg.HTTP.Root, "/")
 			}
 
-			// When running on single binary mode the before hook from the root command won't get called. We manually
-			// call this before hook from ocis command, so the configuration can be loaded.
-			if !cfg.Supervised {
-				return ParseConfig(ctx, cfg)
+			if err := ParseConfig(ctx, cfg); err != nil {
+				return err
 			}
-			logger.Debug().Str("service", "graph-explorer").Msg("ignoring config file parsing when running supervised")
+
 			return nil
 		},
 		Action: func(c *cli.Context) error {
diff --git a/graph-explorer/pkg/config/config.go b/graph-explorer/pkg/config/config.go
index 12653c78c2..8b50a3115b 100644
--- a/graph-explorer/pkg/config/config.go
+++ b/graph-explorer/pkg/config/config.go
@@ -1,6 +1,12 @@
 package config
 
-import "context"
+import (
+	"context"
+	"fmt"
+	"reflect"
+
+	gofig "github.com/gookit/config/v2"
+)
 
 // Log defines the available logging configuration.
 type Log struct {
@@ -66,3 +72,80 @@ type Config struct {
 func New() *Config {
 	return &Config{}
 }
+
+// DefaultConfig provides with a working version of a config.
+func DefaultConfig() *Config {
+	return &Config{
+		Log: Log{},
+		Debug: Debug{
+			Addr:   "127.0.0.1:9136",
+			Token:  "",
+			Pprof:  false,
+			Zpages: false,
+		},
+		HTTP: HTTP{
+			Addr:      "127.0.0.1:9135",
+			Root:      "/graph-explorer",
+			Namespace: "com.owncloud.web",
+		},
+		Server: Server{},
+		Tracing: Tracing{
+			Type:      "jaeger",
+			Endpoint:  "",
+			Collector: "",
+			Service:   "graph-explorer",
+		},
+		GraphExplorer: GraphExplorer{
+			ClientID:     "ocis-explorer.js",
+			Issuer:       "https://localhost:9200",
+			GraphURLBase: "https://localhost:9200",
+			GraphURLPath: "/graph",
+		},
+	}
+}
+
+// GetEnv fetches a list of known env variables for this extension. It is to be used by gookit, as it provides a list
+// with all the environment variables an extension supports.
+func GetEnv() []string {
+	var r = make([]string, len(structMappings(&Config{})))
+	for i := range structMappings(&Config{}) {
+		r = append(r, structMappings(&Config{})[i].EnvVars...)
+	}
+
+	return r
+}
+
+// UnmapEnv loads values from the gooconf.Config argument and sets them in the expected destination.
+func (c *Config) UnmapEnv(gooconf *gofig.Config) error {
+	vals := structMappings(c)
+	for i := range vals {
+		for j := range vals[i].EnvVars {
+			// we need to guard against v != "" because this is the condition that checks that the value is set from the environment.
+			// the `ok` guard is not enough, apparently.
+			if v, ok := gooconf.GetValue(vals[i].EnvVars[j]); ok && v != "" {
+
+				// get the destination type from destination
+				switch reflect.ValueOf(vals[i].Destination).Type().String() {
+				case "*bool":
+					r := gooconf.Bool(vals[i].EnvVars[j])
+					*vals[i].Destination.(*bool) = r
+				case "*string":
+					r := gooconf.String(vals[i].EnvVars[j])
+					*vals[i].Destination.(*string) = r
+				case "*int":
+					r := gooconf.Int(vals[i].EnvVars[j])
+					*vals[i].Destination.(*int) = r
+				case "*float64":
+					// defaults to float64
+					r := gooconf.Float(vals[i].EnvVars[j])
+					*vals[i].Destination.(*float64) = r
+				default:
+					// it is unlikely we will ever get here. Let this serve more as a runtime check for when debugging.
+					return fmt.Errorf("invalid type for env var: `%v`", vals[i].EnvVars[j])
+				}
+			}
+		}
+	}
+
+	return nil
+}
diff --git a/graph-explorer/pkg/config/env.go b/graph-explorer/pkg/config/env.go
new file mode 100644
index 0000000000..f36e9d83ae
--- /dev/null
+++ b/graph-explorer/pkg/config/env.go
@@ -0,0 +1,80 @@
+package config
+
+type mapping struct {
+	EnvVars     []string    // name of the EnvVars var.
+	Destination interface{} // memory address of the original config value to modify.
+}
+
+// structMappings binds a set of environment variables to a destination on cfg.
+func structMappings(cfg *Config) []mapping {
+	return []mapping{
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_LOG_FILE", "OCIS_LOG_FILE"},
+			Destination: &cfg.Log.File,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_ENABLED", "OCIS_TRACING_ENABLED"},
+			Destination: &cfg.Tracing.Enabled,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_TYPE", "OCIS_TRACING_TYPE"},
+			Destination: &cfg.Tracing.Type,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_ENDPOINT", "OCIS_TRACING_ENDPOINT"},
+			Destination: &cfg.Tracing.Endpoint,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_COLLECTOR", "OCIS_TRACING_COLLECTOR"},
+			Destination: &cfg.Tracing.Collector,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_SERVICE"},
+			Destination: &cfg.Tracing.Service,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_ADDR"},
+			Destination: &cfg.Debug.Addr,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_TOKEN"},
+			Destination: &cfg.Debug.Token,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_PPROF"},
+			Destination: &cfg.Debug.Pprof,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_ZPAGES"},
+			Destination: &cfg.Debug.Zpages,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_HTTP_ADDR"},
+			Destination: &cfg.HTTP.Addr,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_HTTP_ROOT"},
+			Destination: &cfg.HTTP.Root,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_NAMESPACE"},
+			Destination: &cfg.HTTP.Namespace,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_ISSUER", "OCIS_URL"},
+			Destination: &cfg.GraphExplorer.Issuer,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_CLIENT_ID"},
+			Destination: &cfg.GraphExplorer.ClientID,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_GRAPH_URL_BASE", "OCIS_URL"},
+			Destination: &cfg.GraphExplorer.GraphURLBase,
+		},
+		{
+			EnvVars:     []string{"GRAPH_EXPLORER_GRAPH_URL_PATH"},
+			Destination: &cfg.GraphExplorer.GraphURLPath,
+		},
+	}
+}
diff --git a/graph-explorer/pkg/flagset/flagset.go b/graph-explorer/pkg/flagset/flagset.go
index 06acd9502a..5215ded0d5 100644
--- a/graph-explorer/pkg/flagset/flagset.go
+++ b/graph-explorer/pkg/flagset/flagset.go
@@ -42,128 +42,3 @@ func HealthWithConfig(cfg *config.Config) []cli.Flag {
 		},
 	}
 }
-
-// ServerWithConfig applies cfg to the root flagset
-func ServerWithConfig(cfg *config.Config) []cli.Flag {
-	return []cli.Flag{
-		&cli.StringFlag{
-			Name:        "log-file",
-			Usage:       "Enable log to file",
-			EnvVars:     []string{"GRAPH_EXPLORER_LOG_FILE", "OCIS_LOG_FILE"},
-			Destination: &cfg.Log.File,
-		},
-		&cli.BoolFlag{
-			Name:        "tracing-enabled",
-			Usage:       "Enable sending traces",
-			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_ENABLED", "OCIS_TRACING_ENABLED"},
-			Destination: &cfg.Tracing.Enabled,
-		},
-		&cli.StringFlag{
-			Name:        "tracing-type",
-			Value:       flags.OverrideDefaultString(cfg.Tracing.Type, "jaeger"),
-			Usage:       "Tracing backend type",
-			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_TYPE", "OCIS_TRACING_TYPE"},
-			Destination: &cfg.Tracing.Type,
-		},
-		&cli.StringFlag{
-			Name:        "tracing-endpoint",
-			Value:       flags.OverrideDefaultString(cfg.Tracing.Endpoint, ""),
-			Usage:       "Endpoint for the agent",
-			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_ENDPOINT", "OCIS_TRACING_ENDPOINT"},
-			Destination: &cfg.Tracing.Endpoint,
-		},
-		&cli.StringFlag{
-			Name:        "tracing-collector",
-			Value:       flags.OverrideDefaultString(cfg.Tracing.Collector, ""),
-			Usage:       "Endpoint for the collector",
-			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_COLLECTOR", "OCIS_TRACING_COLLECTOR"},
-			Destination: &cfg.Tracing.Collector,
-		},
-		&cli.StringFlag{
-			Name:        "tracing-service",
-			Value:       flags.OverrideDefaultString(cfg.Tracing.Service, "graph-explorer"),
-			Usage:       "Service name for tracing",
-			EnvVars:     []string{"GRAPH_EXPLORER_TRACING_SERVICE"},
-			Destination: &cfg.Tracing.Service,
-		},
-		&cli.StringFlag{
-			Name:        "debug-addr",
-			Value:       flags.OverrideDefaultString(cfg.Debug.Addr, "127.0.0.1:9136"),
-			Usage:       "Address to bind debug server",
-			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_ADDR"},
-			Destination: &cfg.Debug.Addr,
-		},
-		&cli.StringFlag{
-			Name:        "debug-token",
-			Value:       flags.OverrideDefaultString(cfg.Debug.Token, ""),
-			Usage:       "Token to grant metrics access",
-			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_TOKEN"},
-			Destination: &cfg.Debug.Token,
-		},
-		&cli.BoolFlag{
-			Name:        "debug-pprof",
-			Usage:       "Enable pprof debugging",
-			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_PPROF"},
-			Destination: &cfg.Debug.Pprof,
-		},
-		&cli.BoolFlag{
-			Name:        "debug-zpages",
-			Usage:       "Enable zpages debugging",
-			EnvVars:     []string{"GRAPH_EXPLORER_DEBUG_ZPAGES"},
-			Destination: &cfg.Debug.Zpages,
-		},
-		&cli.StringFlag{
-			Name:        "http-addr",
-			Value:       flags.OverrideDefaultString(cfg.HTTP.Addr, "127.0.0.1:9135"),
-			Usage:       "Address to bind http server",
-			EnvVars:     []string{"GRAPH_EXPLORER_HTTP_ADDR"},
-			Destination: &cfg.HTTP.Addr,
-		},
-		&cli.StringFlag{
-			Name:        "http-root",
-			Value:       flags.OverrideDefaultString(cfg.HTTP.Root, "/graph-explorer"),
-			Usage:       "Root path of http server",
-			EnvVars:     []string{"GRAPH_EXPLORER_HTTP_ROOT"},
-			Destination: &cfg.HTTP.Root,
-		},
-		&cli.StringFlag{
-			Name:        "http-namespace",
-			Value:       flags.OverrideDefaultString(cfg.HTTP.Namespace, "com.owncloud.web"),
-			Usage:       "Set the base namespace for the http namespace",
-			EnvVars:     []string{"GRAPH_EXPLORER_NAMESPACE"},
-			Destination: &cfg.HTTP.Namespace,
-		},
-		&cli.StringFlag{
-			Name:        "issuer",
-			Value:       flags.OverrideDefaultString(cfg.GraphExplorer.Issuer, "https://localhost:9200"),
-			Usage:       "Set the OpenID Connect Provider",
-			EnvVars:     []string{"GRAPH_EXPLORER_ISSUER", "OCIS_URL"},
-			Destination: &cfg.GraphExplorer.Issuer,
-		},
-		&cli.StringFlag{
-			Name:        "client-id",
-			Value:       flags.OverrideDefaultString(cfg.GraphExplorer.ClientID, "ocis-explorer.js"),
-			Usage:       "Set the OpenID Client ID to send to the issuer",
-			EnvVars:     []string{"GRAPH_EXPLORER_CLIENT_ID"},
-			Destination: &cfg.GraphExplorer.ClientID,
-		},
-		&cli.StringFlag{
-			Name:        "graph-url-base",
-			Value:       flags.OverrideDefaultString(cfg.GraphExplorer.GraphURLBase, "https://localhost:9200"),
-			Usage:       "Set the base url to the graph api service",
-			EnvVars:     []string{"GRAPH_EXPLORER_GRAPH_URL_BASE", "OCIS_URL"},
-			Destination: &cfg.GraphExplorer.GraphURLBase,
-		},
-		&cli.StringFlag{
-			Name:        "graph-url-path",
-			Value:       flags.OverrideDefaultString(cfg.GraphExplorer.GraphURLPath, "/graph"),
-			Usage:       "Set the url path to the graph api service",
-			EnvVars:     []string{"GRAPH_EXPLORER_GRAPH_URL_PATH"},
-			Destination: &cfg.GraphExplorer.GraphURLPath,
-		},
-		&cli.StringFlag{
-			Name:  "extensions",
-			Usage: "Run specific extensions during supervised mode. This flag is set by the runtime",
-		},
-	}
-}
diff --git a/graph/pkg/command/server.go b/graph/pkg/command/server.go
index 480adca305..cf4b638127 100644
--- a/graph/pkg/command/server.go
+++ b/graph/pkg/command/server.go
@@ -24,8 +24,6 @@ func Server(cfg *config.Config) *cli.Command {
 				cfg.HTTP.Root = strings.TrimSuffix(cfg.HTTP.Root, "/")
 			}
 
-			// When running on single binary mode the before hook from the root command won't get called. We manually
-			// call this before hook from ocis command, so the configuration can be loaded.
 			if err := ParseConfig(ctx, cfg); err != nil {
 				return err
 			}
diff --git a/ocis-pkg/config/config.go b/ocis-pkg/config/config.go
index 81c593d024..74771ce4dd 100644
--- a/ocis-pkg/config/config.go
+++ b/ocis-pkg/config/config.go
@@ -119,7 +119,7 @@ func New() *Config {
 		Graph:         graph.DefaultConfig(),
 		IDP:           idp.DefaultConfig(),
 		Proxy:         proxy.DefaultConfig(),
-		GraphExplorer: graphExplorer.New(),
+		GraphExplorer: graphExplorer.DefaultConfig(),
 		OCS:           ocs.New(),
 		Web:           web.New(),
 		Settings:      settings.New(),