diff --git a/dvid/utils.go b/dvid/utils.go
index 2278d186..d70c88ce 100644
--- a/dvid/utils.go
+++ b/dvid/utils.go
@@ -147,6 +147,22 @@ func (fname Filename) HasExtensionPrefix(exts ...string) bool {
 	return false
 }
 
+// Converts the given (possibly) relative path into an absolute path,
+// relative to the given anchor directory, not the current working directory.
+// If the given relativePath is already an absolute path,
+// it is returned unchanged.
+func ConvertToAbsolute(relativePath string, anchorDir string) (string, error) {
+	if filepath.IsAbs(relativePath) {
+		return relativePath, nil
+	}
+	absDir, err := filepath.Abs(anchorDir)
+	if err != nil {
+		return relativePath, fmt.Errorf("Could not decode TOML config: %v\n", err)
+	}
+	absPath := filepath.Join(absDir, relativePath)
+	return absPath, nil
+}
+
 // DataFromPost returns data submitted in the given key of a POST request.
 func DataFromPost(r *http.Request, key string) ([]byte, error) {
 	f, _, err := r.FormFile(key)
diff --git a/server/server_local.go b/server/server_local.go
index f452cfff..398828d2 100644
--- a/server/server_local.go
+++ b/server/server_local.go
@@ -11,6 +11,7 @@ package server
 import (
 	"bytes"
 	"fmt"
+	"path/filepath"
 	"net/smtp"
 	"os"
 	"os/exec"
@@ -68,6 +69,45 @@ type tomlConfig struct {
 	Groupcache storage.GroupcacheConfig
 }
 
+// Some settings in the TOML can be given as relative paths.
+// This function converts them in-place to absolute paths,
+// assuming the given paths were relative to the TOML file's own directory.
+func (c *tomlConfig) ConvertPathsToAbsolute(configPath string) error {
+	var err error
+
+	configDir := filepath.Dir(configPath)
+	
+	// [server].webClient
+	c.Server.WebClient, err = dvid.ConvertToAbsolute(c.Server.WebClient, configDir)
+	if err != nil {
+		return fmt.Errorf("Error converting webClient setting to absolute path")
+	}
+	
+	// [logging].logfile
+	c.Logging.Logfile, err = dvid.ConvertToAbsolute(c.Logging.Logfile, configDir)
+	if err != nil {
+		return fmt.Errorf("Error converting logfile setting to absolute path")
+	}
+
+	// [store.foobar].path
+	for alias, sc := range c.Store {
+		p, ok := sc["path"]
+		if !ok {
+			continue
+		}
+		path, ok := p.(string)
+		if !ok {
+			return fmt.Errorf("Don't understand path setting for store %q", alias)
+		}
+		absPath, err := dvid.ConvertToAbsolute(path, configDir)
+		if err != nil {
+			return fmt.Errorf("Error converting store.%s.path to absolute path: %q", alias, path)
+		}
+		sc["path"] = absPath
+	}
+	return nil
+}
+
 func (c tomlConfig) Stores() (map[storage.Alias]dvid.StoreConfig, error) {
 	stores := make(map[storage.Alias]dvid.StoreConfig, len(c.Store))
 	for alias, sc := range c.Store {
@@ -154,11 +194,15 @@ func LoadConfig(filename string) (*datastore.InstanceConfig, *dvid.LogConfig, *s
 	if _, err := toml.DecodeFile(filename, &tc); err != nil {
 		return nil, nil, nil, fmt.Errorf("Could not decode TOML config: %v\n", err)
 	}
+	var err error
+	err = tc.ConvertPathsToAbsolute(filename)
+	if err != nil {
+		return nil, nil, nil, fmt.Errorf("Could not convert relative paths to absolute paths in TOML config: %v\n", err)
+	}
 
 	// Get all defined stores.
 	backend := new(storage.Backend)
 	backend.Groupcache = tc.Groupcache
-	var err error
 	backend.Stores, err = tc.Stores()
 	if err != nil {
 		return nil, nil, nil, err
diff --git a/server/server_local_test.go b/server/server_local_test.go
index cb51f8d0..ad6abcd3 100644
--- a/server/server_local_test.go
+++ b/server/server_local_test.go
@@ -4,6 +4,7 @@ import (
 	"io/ioutil"
 	"os"
 	"testing"
+	"github.com/janelia-flyem/dvid/storage"
 )
 
 func loadConfigFile(t *testing.T, filename string) string {
@@ -35,3 +36,49 @@ func TestParseConfig(t *testing.T) {
 		t.Errorf("Bad backend configuration retrieval: %v\n", backendCfg)
 	}
 }
+
+func TestTOMLConfigAbsolutePath(t *testing.T) {
+	// Initialize the filepath settings
+	var c tomlConfig
+	c.Server.WebClient = "dvid-distro/dvid-console"
+	c.Logging.Logfile = "./foobar.log"
+
+	c.Store = make(map[storage.Alias]storeConfig)
+
+	c.Store["foo"] = make(storeConfig)
+	c.Store["foo"]["engine"] = "basholeveldb"
+	c.Store["foo"]["path"] = "foo-storage-db"
+
+	c.Store["bar"] = make(storeConfig)
+	c.Store["bar"]["engine"] = "basholeveldb"
+	c.Store["bar"]["path"] = "/tmp/bar-storage-db" // Already absolute, should stay unchanged.
+
+	// Convert relative paths to absolute
+	c.ConvertPathsToAbsolute("/tmp/dvid-configs/myconfig.toml")
+
+	// Checks
+	if c.Server.WebClient != "/tmp/dvid-configs/dvid-distro/dvid-console" {
+		t.Errorf("WebClient not correctly converted to absolute path: %s", c.Server.WebClient)
+	}
+
+	if c.Logging.Logfile != "/tmp/dvid-configs/foobar.log" {
+		t.Errorf("Logfile not correctly converted to absolute path: %s", c.Logging.Logfile)
+	}
+
+	foo, _ := c.Store["foo"]
+	path, _ := foo["path"]
+	if path.(string) != "/tmp/dvid-configs/foo-storage-db" {
+		t.Errorf("[store.foo].path not correctly converted to absolute path: %s", path)
+	}
+
+	engine, _ := foo["engine"]
+	if engine.(string) != "basholeveldb" {
+		t.Errorf("[store.foo].engine should not have been touched: %s", path)
+	}
+
+	bar, _ := c.Store["bar"]
+	path, _ = bar["path"]
+	if path.(string) != "/tmp/bar-storage-db" {
+		t.Errorf("[store.bar].path was already absolute and should have been left unchanged: %s", path)
+	}
+}