diff --git a/cmd/prometheus/main.go b/cmd/prometheus/main.go
index 495254b9d..214ba7d75 100644
--- a/cmd/prometheus/main.go
+++ b/cmd/prometheus/main.go
@@ -21,7 +21,6 @@ import (
 	_ "net/http/pprof" // Comment this line to disable pprof endpoint.
 	"os"
 	"os/signal"
-	"path/filepath"
 	"strings"
 	"syscall"
 	"text/template"
@@ -77,7 +76,6 @@ func Main() int {
 		NotificationHandler: notificationHandler,
 		QueryEngine:         queryEngine,
 		ExternalURL:         cfg.web.ExternalURL,
-		BaseDir:             filepath.Dir(cfg.configFile),
 	})
 
 	flags := map[string]string{}
diff --git a/config/config.go b/config/config.go
index 136a4f898..dc0fdca7e 100644
--- a/config/config.go
+++ b/config/config.go
@@ -5,6 +5,7 @@ import (
 	"fmt"
 	"io/ioutil"
 	"net/url"
+	"path/filepath"
 	"regexp"
 	"strings"
 	"time"
@@ -45,7 +46,12 @@ func LoadFromFile(filename string) (*Config, error) {
 	if err != nil {
 		return nil, err
 	}
-	return Load(string(content))
+	cfg, err := Load(string(content))
+	if err != nil {
+		return nil, err
+	}
+	resolveFilepaths(filepath.Dir(filename), cfg)
+	return cfg, nil
 }
 
 // The defaults applied before parsing the respective config sections.
@@ -113,6 +119,30 @@ type Config struct {
 	original string
 }
 
+// resolveFilepaths joins all relative paths in a configuration
+// with a given base directory.
+func resolveFilepaths(baseDir string, cfg *Config) {
+	join := func(fp string) string {
+		if len(fp) > 0 && !filepath.IsAbs(fp) {
+			fp = filepath.Join(baseDir, fp)
+		}
+		return fp
+	}
+
+	for i, rf := range cfg.RuleFiles {
+		cfg.RuleFiles[i] = join(rf)
+	}
+
+	for _, scfg := range cfg.ScrapeConfigs {
+		scfg.BearerTokenFile = join(scfg.BearerTokenFile)
+
+		if scfg.ClientCert != nil {
+			scfg.ClientCert.Cert = join(scfg.ClientCert.Cert)
+			scfg.ClientCert.Key = join(scfg.ClientCert.Key)
+		}
+	}
+}
+
 func checkOverflow(m map[string]interface{}, ctx string) error {
 	if len(m) > 0 {
 		var keys []string
diff --git a/config/config_test.go b/config/config_test.go
index 64436fb36..5284699fa 100644
--- a/config/config_test.go
+++ b/config/config_test.go
@@ -27,9 +27,9 @@ var expectedConf = &Config{
 	},
 
 	RuleFiles: []string{
-		"first.rules",
-		"second.rules",
-		"my/*.rules",
+		"testdata/first.rules",
+		"/absolute/second.rules",
+		"testdata/my/*.rules",
 	},
 
 	ScrapeConfigs: []*ScrapeConfig{
@@ -43,6 +43,8 @@ var expectedConf = &Config{
 			MetricsPath: DefaultScrapeConfig.MetricsPath,
 			Scheme:      DefaultScrapeConfig.Scheme,
 
+			BearerTokenFile: "testdata/valid_token_file",
+
 			TargetGroups: []*TargetGroup{
 				{
 					Targets: []clientmodel.LabelSet{
@@ -167,8 +169,8 @@ var expectedConf = &Config{
 			Scheme:      "http",
 
 			ClientCert: &ClientCert{
-				Cert: "valid_cert_file",
-				Key:  "valid_key_file",
+				Cert: "testdata/valid_cert_file",
+				Key:  "testdata/valid_key_file",
 			},
 			BearerToken: "avalidtoken",
 		},
diff --git a/config/testdata/conf.good.yml b/config/testdata/conf.good.yml
index df8cf62c6..33475960f 100644
--- a/config/testdata/conf.good.yml
+++ b/config/testdata/conf.good.yml
@@ -10,7 +10,7 @@ global:
 
 rule_files:
 - "first.rules"
-- "second.rules"
+- "/absolute/second.rules"
 - "my/*.rules"
 
 scrape_configs:
@@ -45,6 +45,8 @@ scrape_configs:
     replacement:   foo-${1}
     # action defaults to 'replace'
 
+  bearer_token_file: valid_token_file
+
 
 - job_name: service-x
 
diff --git a/rules/manager.go b/rules/manager.go
index c862fe677..1dccfcf5c 100644
--- a/rules/manager.go
+++ b/rules/manager.go
@@ -104,7 +104,6 @@ type Manager struct {
 	notificationHandler *notification.NotificationHandler
 
 	externalURL *url.URL
-	baseDir     string
 }
 
 // ManagerOptions bundles options for the Manager.
@@ -116,7 +115,6 @@ type ManagerOptions struct {
 	SampleAppender      storage.SampleAppender
 
 	ExternalURL *url.URL
-	BaseDir     string
 }
 
 // NewManager returns an implementation of Manager, ready to be started
@@ -131,7 +129,6 @@ func NewManager(o *ManagerOptions) *Manager {
 		queryEngine:         o.QueryEngine,
 		notificationHandler: o.NotificationHandler,
 		externalURL:         o.ExternalURL,
-		baseDir:             o.BaseDir,
 	}
 	return manager
 }
@@ -330,10 +327,6 @@ func (m *Manager) ApplyConfig(conf *config.Config) bool {
 
 	var files []string
 	for _, pat := range conf.RuleFiles {
-		if !filepath.IsAbs(pat) {
-			pat = filepath.Join(m.baseDir, pat)
-		}
-
 		fs, err := filepath.Glob(pat)
 		if err != nil {
 			// The only error can be a bad pattern.