diff --git a/changelog.md b/changelog.md
index e861b4c43..8b8a545b7 100644
--- a/changelog.md
+++ b/changelog.md
@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 ### Changed
+- [Fixed the issue related to existing configurations in Config.toml file](https://github.com/ballerina-platform/persist-tools/issues/314)
 - [Fix the logic in persist client generation with respect to refColumns in the joinMetadata](https://github.com/ballerina-platform/persist-tools/issues/312)
 
 ## [1.2.0] - 2023-09-19
diff --git a/persist-cli-tests/src/test/resources/test-src/input/tool_test_generate_5/Config.toml b/persist-cli-tests/src/test/resources/test-src/input/tool_test_generate_5/Config.toml
index dddc88d62..71c3b04d0 100644
--- a/persist-cli-tests/src/test/resources/test-src/input/tool_test_generate_5/Config.toml
+++ b/persist-cli-tests/src/test/resources/test-src/input/tool_test_generate_5/Config.toml
@@ -4,3 +4,6 @@ port = 3306
 user = "root"
 password = ""
 database = ""
+
+[persist_generate_5.connectionOptions.ssl]
+allowPublicKeyRetrieval=true
diff --git a/persist-cli-tests/src/test/resources/test-src/output/tool_test_generate_5/Config.toml b/persist-cli-tests/src/test/resources/test-src/output/tool_test_generate_5/Config.toml
index 0616ed500..71c3b04d0 100644
--- a/persist-cli-tests/src/test/resources/test-src/output/tool_test_generate_5/Config.toml
+++ b/persist-cli-tests/src/test/resources/test-src/output/tool_test_generate_5/Config.toml
@@ -5,3 +5,5 @@ user = "root"
 password = ""
 database = ""
 
+[persist_generate_5.connectionOptions.ssl]
+allowPublicKeyRetrieval=true
diff --git a/persist-cli/src/main/java/io/ballerina/persist/nodegenerator/SourceGenerator.java b/persist-cli/src/main/java/io/ballerina/persist/nodegenerator/SourceGenerator.java
index 632d585c6..513d77be5 100644
--- a/persist-cli/src/main/java/io/ballerina/persist/nodegenerator/SourceGenerator.java
+++ b/persist-cli/src/main/java/io/ballerina/persist/nodegenerator/SourceGenerator.java
@@ -254,7 +254,6 @@ private SyntaxTree getUpdateConfigTomlSyntax(Path configPath, String moduleName,
                     moduleMembers = moduleMembers.add(member);
                     if (node.identifier().toSourceCode().trim().equals(moduleName)) {
                         configExists = true;
-                        break;
                     }
                 } else if (member instanceof TableArrayNode) {
                     moduleMembers = moduleMembers.add(member);