diff --git a/config/reload.go b/config/reload.go
index 8be1b28d8..3283b425f 100644
--- a/config/reload.go
+++ b/config/reload.go
@@ -19,6 +19,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 
 	"gopkg.in/yaml.v2"
 )
@@ -49,10 +50,15 @@ func GenerateChecksum(yamlFilePath string) (string, error) {
 	dir := filepath.Dir(yamlFilePath)
 
 	for i, file := range config.RuleFiles {
-		config.RuleFiles[i] = filepath.Join(dir, file)
+		if !strings.Contains(config.RuleFiles[i], dir) {
+			config.RuleFiles[i] = filepath.Join(dir, file) // Join the directory only if the parent directory is not present in the config
+		}
 	}
+
 	for i, file := range config.ScrapeConfigFiles {
-		config.ScrapeConfigFiles[i] = filepath.Join(dir, file)
+		if !strings.Contains(config.ScrapeConfigFiles[i], dir) {
+			config.ScrapeConfigFiles[i] = filepath.Join(dir, file) // Join the directory only if the parent directory is not present in the config
+		}
 	}
 
 	files := map[string][]string{
diff --git a/config/reload_test.go b/config/reload_test.go
index f0f44f358..851536ba8 100644
--- a/config/reload_test.go
+++ b/config/reload_test.go
@@ -40,8 +40,12 @@ func TestGenerateChecksum(t *testing.T) {
 	yamlContent := `
 rule_files:
   - rule_file.yml
+  - /etc/prometheus/rules/rule_file.yml
+  - /etc/prometheus/rules/glob/*.yml
 scrape_config_files:
   - scrape_config.yml
+  - /etc/prometheus/scrape_config_files/scrape_config.yml
+  - /etc/prometheus/scrape_config_files/glob/*.yml
 `
 
 	// Write initial content to files.
@@ -123,8 +127,12 @@ global:
   scrape_interval: 3s
 rule_files:
   - rule_file.yml
+  - /etc/prometheus/rules/rule_file.yml
+  - /etc/prometheus/rules/glob/*.yml
 scrape_config_files:
   - scrape_config.yml
+  - /etc/prometheus/scrape_config_files/scrape_config.yml
+  - /etc/prometheus/scrape_config_files/glob/*.yml
 `
 		require.NoError(t, os.WriteFile(yamlFilePath, []byte(modifiedYamlContent), 0o644))
 
@@ -145,6 +153,8 @@ scrape_config_files:
 		modifiedYamlContent := `
 scrape_config_files:
   - scrape_config.yml
+  - /etc/prometheus/scrape_config_files/scrape_config.yml
+  - /etc/prometheus/scrape_config_files/glob/*.yml
 `
 		require.NoError(t, os.WriteFile(yamlFilePath, []byte(modifiedYamlContent), 0o644))
 
@@ -165,6 +175,8 @@ scrape_config_files:
 		modifiedYamlContent := `
 rule_files:
   - rule_file.yml
+  - /etc/prometheus/rules/rule_file.yml
+  - /etc/prometheus/rules/glob/*.yml
 `
 		require.NoError(t, os.WriteFile(yamlFilePath, []byte(modifiedYamlContent), 0o644))