diff --git a/CHANGELOG.md b/CHANGELOG.md
index 68765cce811..833f79bddb6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,7 @@ The order and collapsed state of columns is now persisted across page navigation
 
 ### Bug fixes and improvements
 
+- cli: allow customization of server api paths (close #4016)
 - cli: clean up migration files created during a failed migrate api (close #4312) (#4319)
 - cli: add support for multiple versions of plugin (close #4105)
 - cli: template assets path in console HTML for unversioned builds
diff --git a/cli/cli.go b/cli/cli.go
index 4a0344e9de3..4a4a4fd5c5a 100644
--- a/cli/cli.go
+++ b/cli/cli.go
@@ -12,7 +12,9 @@ import (
 	"io/ioutil"
 	"net/url"
 	"os"
+	"path"
 	"path/filepath"
+	"reflect"
 	"strconv"
 	"strings"
 	"time"
@@ -61,6 +63,36 @@ const (
 	V2
 )
 
+// ServerAPIPaths has the custom paths defined for server api
+type ServerAPIPaths struct {
+	Query   string `yaml:"query,omitempty"`
+	GraphQL string `yaml:"graphql,omitempty"`
+	Config  string `yaml:"config,omitempty"`
+	PGDump  string `yaml:"pg_dump,omitempty"`
+	Version string `yaml:"version,omitempty"`
+}
+
+// GetQueryParams - encodes the values in url
+func (s ServerAPIPaths) GetQueryParams() url.Values {
+	vals := url.Values{}
+	t := reflect.TypeOf(s)
+	for i := 0; i < t.NumField(); i++ {
+		field := t.Field(i)
+		tag := field.Tag.Get("yaml")
+		splitTag := strings.Split(tag, ",")
+		if len(splitTag) == 0 {
+			continue
+		}
+		name := splitTag[0]
+		if name == "-" {
+			continue
+		}
+		v := reflect.ValueOf(s).Field(i)
+		vals.Add(name, v.String())
+	}
+	return vals
+}
+
 // ErrInvalidConfigVersion - if the config version is not valid
 var ErrInvalidConfigVersion error = fmt.Errorf("invalid config version")
 
@@ -105,10 +137,19 @@ type ServerConfig struct {
 	AccessKey string `yaml:"access_key,omitempty"`
 	// AdminSecret (optional) Admin secret required to query the endpoint
 	AdminSecret string `yaml:"admin_secret,omitempty"`
+	// APIPaths (optional) API paths for server
+	APIPaths *ServerAPIPaths `yaml:"api_paths,omitempty"`
 
 	ParsedEndpoint *url.URL `yaml:"-"`
 }
 
+// GetVersionEndpoint provides the url to contact the version API
+func (s *ServerConfig) GetVersionEndpoint() string {
+	nurl := *s.ParsedEndpoint
+	nurl.Path = path.Join(nurl.Path, s.APIPaths.Version)
+	return nurl.String()
+}
+
 // ParseEndpoint ensures the endpoint is valid.
 func (s *ServerConfig) ParseEndpoint() error {
 	nurl, err := url.Parse(s.Endpoint)
@@ -398,7 +439,7 @@ func (ec *ExecutionContext) Validate() error {
 }
 
 func (ec *ExecutionContext) checkServerVersion() error {
-	v, err := version.FetchServerVersion(ec.Config.ServerConfig.Endpoint)
+	v, err := version.FetchServerVersion(ec.Config.ServerConfig.GetVersionEndpoint())
 	if err != nil {
 		return errors.Wrap(err, "failed to get version from server")
 	}
@@ -441,6 +482,11 @@ func (ec *ExecutionContext) readConfig() error {
 	v.SetDefault("endpoint", "http://localhost:8080")
 	v.SetDefault("admin_secret", "")
 	v.SetDefault("access_key", "")
+	v.SetDefault("api_paths.query", "v1/query")
+	v.SetDefault("api_paths.graphql", "v1/graphql")
+	v.SetDefault("api_paths.config", "v1alpha1/config")
+	v.SetDefault("api_paths.pg_dump", "v1alpha1/pg_dump")
+	v.SetDefault("api_paths.version", "v1/version")
 	v.SetDefault("metadata_directory", "")
 	v.SetDefault("migrations_directory", "migrations")
 	v.SetDefault("actions.kind", "synchronous")
@@ -462,6 +508,13 @@ func (ec *ExecutionContext) readConfig() error {
 		ServerConfig: ServerConfig{
 			Endpoint:    v.GetString("endpoint"),
 			AdminSecret: adminSecret,
+			APIPaths: &ServerAPIPaths{
+				Query:   v.GetString("api_paths.query"),
+				GraphQL: v.GetString("api_paths.graphql"),
+				Config:  v.GetString("api_paths.config"),
+				PGDump:  v.GetString("api_paths.pg_dump"),
+				Version: v.GetString("api_paths.version"),
+			},
 		},
 		MetadataDirectory:   v.GetString("metadata_directory"),
 		MigrationsDirectory: v.GetString("migrations_directory"),
diff --git a/cli/commands/scripts_update_config_v2.go b/cli/commands/scripts_update_config_v2.go
index 30d778e7bc7..61b38eb56df 100644
--- a/cli/commands/scripts_update_config_v2.go
+++ b/cli/commands/scripts_update_config_v2.go
@@ -12,6 +12,7 @@ import (
 	"gopkg.in/yaml.v2"
 
 	"github.com/hasura/graphql-engine/cli"
+	"github.com/hasura/graphql-engine/cli/metadata/actions/types"
 	"github.com/hasura/graphql-engine/cli/migrate/database/hasuradb"
 	"github.com/hasura/graphql-engine/cli/migrate/source"
 	"github.com/hasura/graphql-engine/cli/migrate/source/file"
@@ -319,7 +320,23 @@ func newScriptsUpdateConfigV2Cmd(ec *cli.ExecutionContext) *cobra.Command {
 				return errors.Wrap(err, "cannot write metadata")
 			}
 			ec.Spin("Writing new config file...")
-			err = ec.WriteConfig(nil)
+			// Read the config from config.yaml
+			cfgByt, err := ioutil.ReadFile(ec.ConfigFile)
+			if err != nil {
+				return errors.Wrap(err, "cannot read config file")
+			}
+			var cfg cli.Config
+			err = yaml.Unmarshal(cfgByt, &cfg)
+			if err != nil {
+				return errors.Wrap(err, "cannot parse config file")
+			}
+			cfg.Version = cli.V2
+			cfg.MetadataDirectory = ec.Viper.GetString("metadata_directory")
+			cfg.ActionConfig = &types.ActionExecutionConfig{
+				Kind:                  ec.Viper.GetString("actions.kind"),
+				HandlerWebhookBaseURL: ec.Viper.GetString("actions.handler_webhook_baseurl"),
+			}
+			err = ec.WriteConfig(&cfg)
 			if err != nil {
 				return errors.Wrap(err, "cannot write config file")
 			}
diff --git a/cli/migrate/database/hasuradb/hasuradb.go b/cli/migrate/database/hasuradb/hasuradb.go
index 60e92f8a8b2..841bdb37415 100644
--- a/cli/migrate/database/hasuradb/hasuradb.go
+++ b/cli/migrate/database/hasuradb/hasuradb.go
@@ -40,9 +40,9 @@ var (
 type Config struct {
 	MigrationsTable string
 	SettingsTable   string
-	v1URL           *nurl.URL
+	queryURL        *nurl.URL
 	graphqlURL      *nurl.URL
-	schemDumpURL    *nurl.URL
+	pgDumpURL       *nurl.URL
 	Headers         map[string]string
 	isCMD           bool
 	Plugins         types.MetadataPlugins
@@ -115,20 +115,20 @@ func (h *HasuraDB) Open(url string, isCMD bool, logger *log.Logger) (database.Dr
 	config := &Config{
 		MigrationsTable: DefaultMigrationsTable,
 		SettingsTable:   DefaultSettingsTable,
-		v1URL: &nurl.URL{
+		queryURL: &nurl.URL{
 			Scheme: scheme,
 			Host:   hurl.Host,
-			Path:   path.Join(hurl.Path, "v1/query"),
+			Path:   path.Join(hurl.Path, params.Get("query")),
 		},
 		graphqlURL: &nurl.URL{
 			Scheme: scheme,
 			Host:   hurl.Host,
-			Path:   path.Join(hurl.Path, "v1/graphql"),
+			Path:   path.Join(hurl.Path, params.Get("graphql")),
 		},
-		schemDumpURL: &nurl.URL{
+		pgDumpURL: &nurl.URL{
 			Scheme: scheme,
 			Host:   hurl.Host,
-			Path:   path.Join(hurl.Path, "v1alpha1/pg_dump"),
+			Path:   path.Join(hurl.Path, params.Get("pg_dump")),
 		},
 		isCMD:   isCMD,
 		Headers: headers,
@@ -417,7 +417,7 @@ func (h *HasuraDB) ensureVersionTable() error {
 
 func (h *HasuraDB) sendv1Query(m interface{}) (resp *http.Response, body []byte, err error) {
 	request := gorequest.New()
-	request = request.Post(h.config.v1URL.String()).Send(m)
+	request = request.Post(h.config.queryURL.String()).Send(m)
 	for headerName, headerValue := range h.config.Headers {
 		request.Set(headerName, headerValue)
 	}
@@ -455,7 +455,7 @@ func (h *HasuraDB) sendv1GraphQL(query interface{}) (resp *http.Response, body [
 func (h *HasuraDB) sendSchemaDumpQuery(m interface{}) (resp *http.Response, body []byte, err error) {
 	request := gorequest.New()
 
-	request = request.Post(h.config.schemDumpURL.String()).Send(m)
+	request = request.Post(h.config.pgDumpURL.String()).Send(m)
 
 	for headerName, headerValue := range h.config.Headers {
 		request.Set(headerName, headerValue)
diff --git a/cli/migrate/util.go b/cli/migrate/util.go
index 0dfda094994..bbed7201eef 100644
--- a/cli/migrate/util.go
+++ b/cli/migrate/util.go
@@ -121,7 +121,7 @@ func FilterCustomQuery(u *nurl.URL) *nurl.URL {
 }
 
 func NewMigrate(ec *cli.ExecutionContext, isCmd bool) (*Migrate, error) {
-	dbURL := GetDataPath(ec.Config.ServerConfig.ParsedEndpoint, GetAdminSecretHeaderName(ec.Version), ec.Config.ServerConfig.AdminSecret)
+	dbURL := GetDataPath(ec)
 	fileURL := GetFilePath(ec.MigrationDir)
 	t, err := New(fileURL.String(), dbURL.String(), isCmd, int(ec.Config.Version), ec.Logger)
 	if err != nil {
@@ -132,13 +132,15 @@ func NewMigrate(ec *cli.ExecutionContext, isCmd bool) (*Migrate, error) {
 	return t, nil
 }
 
-func GetDataPath(url *nurl.URL, adminSecretHeader, adminSecretValue string) *nurl.URL {
+func GetDataPath(ec *cli.ExecutionContext) *nurl.URL {
+	url := ec.Config.ServerConfig.ParsedEndpoint
 	host := &nurl.URL{
-		Scheme: "hasuradb",
-		Host:   url.Host,
-		Path:   url.Path,
+		Scheme:   "hasuradb",
+		Host:     url.Host,
+		Path:     url.Path,
+		RawQuery: ec.Config.ServerConfig.APIPaths.GetQueryParams().Encode(),
 	}
-	q := url.Query()
+	q := host.Query()
 	// Set sslmode in query
 	switch scheme := url.Scheme; scheme {
 	case "https":
@@ -146,8 +148,8 @@ func GetDataPath(url *nurl.URL, adminSecretHeader, adminSecretValue string) *nur
 	default:
 		q.Set("sslmode", "disable")
 	}
-	if adminSecretValue != "" {
-		q.Add("headers", fmt.Sprintf("%s:%s", adminSecretHeader, adminSecretValue))
+	if GetAdminSecretHeaderName(ec.Version) != "" {
+		q.Add("headers", fmt.Sprintf("%s:%s", GetAdminSecretHeaderName(ec.Version), ec.Config.ServerConfig.AdminSecret))
 	}
 	host.RawQuery = q.Encode()
 	return host
diff --git a/cli/version/server.go b/cli/version/server.go
index 1fa5f26620e..c1b2f8a928a 100644
--- a/cli/version/server.go
+++ b/cli/version/server.go
@@ -1,10 +1,8 @@
 package version
 
 import (
-	"fmt"
 	"io/ioutil"
 	"net/http"
-	"net/url"
 
 	yaml "github.com/ghodss/yaml"
 	"github.com/pkg/errors"
@@ -16,12 +14,7 @@ type serverVersionResponse struct {
 
 // FetchServerVersion reads the version from server.
 func FetchServerVersion(endpoint string) (version string, err error) {
-	ep, err := url.Parse(endpoint)
-	if err != nil {
-		return "", errors.Wrap(err, "cannot parse endpoint as a valid url")
-	}
-	versionEndpoint := fmt.Sprintf("%s/v1/version", ep.String())
-	response, err := http.Get(versionEndpoint)
+	response, err := http.Get(endpoint)
 	if err != nil {
 		return "", errors.Wrap(err, "failed making version api call")
 	}
@@ -30,7 +23,7 @@ func FetchServerVersion(endpoint string) (version string, err error) {
 		case http.StatusNotFound:
 			return "", nil
 		default:
-			return "", errors.Errorf("GET %s failed - [%d]", versionEndpoint, response.StatusCode)
+			return "", errors.Errorf("GET %s failed - [%d]", endpoint, response.StatusCode)
 		}
 	} else {
 		defer response.Body.Close()