diff --git a/pkg/common/file.go b/pkg/common/file.go
index e57e58d0da..8637fc4850 100644
--- a/pkg/common/file.go
+++ b/pkg/common/file.go
@@ -182,9 +182,9 @@ func setConfigOption(configName, configValue string, yamlData *yaml.Node) {
 	for indx := 0; indx < contentLen-1; {
 		name := yamlData.Content[0].Content[indx].Value
 		if name == configName {
+			// Set the value, even if we have the option defined multiple times.
 			yamlData.Content[0].Content[indx+1].Value = configValue
 			foundOption = true
-			break
 		}
 		indx += 2
 	}
diff --git a/test/e2e/config_test.go b/test/e2e/config_test.go
index 822b9c9fc4..8c9043fa8e 100644
--- a/test/e2e/config_test.go
+++ b/test/e2e/config_test.go
@@ -87,4 +87,42 @@ pull-image-on-create: false
 disable-pull-on-run: false
 `))
 	})
+
+	It("should succeed to get the right value if duplicate entries are defined", func() {
+		_, err := configFile.WriteString(`
+timeout: 20
+timeout: 5
+timeout: 10
+`)
+		Expect(err).NotTo(HaveOccurred())
+
+		t.CrictlExpectSuccess("--config "+configFile.Name()+" config --get timeout", "10")
+	})
+
+	It("should succeed to set duplicate entries", func() {
+		_, err := configFile.WriteString(`
+timeout: 20
+timeout: 5
+timeout: 10
+`)
+		Expect(err).NotTo(HaveOccurred())
+
+		t.CrictlExpectSuccess("--config "+configFile.Name()+" config --set timeout=30", "")
+
+		cfgContent, err := os.ReadFile(configFile.Name())
+		Expect(err).NotTo(HaveOccurred())
+
+		Expect(string(cfgContent)).To(Equal(
+			`timeout: 30
+timeout: 30
+timeout: 30
+runtime-endpoint: ""
+image-endpoint: ""
+debug: false
+pull-image-on-create: false
+disable-pull-on-run: false
+`))
+
+		t.CrictlExpectSuccess("--config "+configFile.Name()+" config --get timeout", "30")
+	})
 })