diff --git a/src/Cli.Tests/UpdateEntityTests.cs b/src/Cli.Tests/UpdateEntityTests.cs
index cac2db0a83..8c823d8eb3 100644
--- a/src/Cli.Tests/UpdateEntityTests.cs
+++ b/src/Cli.Tests/UpdateEntityTests.cs
@@ -1100,6 +1100,85 @@ public void TestUpdateEntityDescription()
             Assert.AreEqual("Updated description", updatedRuntimeConfig.Entities["MyEntity"].Description);
         }
 
+        /// <summary>
+        /// Updating a field's description without --fields.primary-key
+        /// should not change its existing primary-key flag.
+        /// </summary>
+        [TestMethod]
+        public void TestUpdateFieldDescriptionPreservesPrimaryKeyWhenNoFlagProvided()
+        {
+            string initialConfig = GetInitialConfigString() + "," + @"
+                ""entities"": {
+                    ""MyEntity"": {
+                        ""source"": ""MyTable"",
+                        ""fields"": [
+                            {
+                                ""name"": ""Id"",
+                                ""description"": ""Primary key"",
+                                ""primary-key"": true
+                            }
+                        ],
+                        ""permissions"": [
+                            {
+                                ""role"": ""anonymous"",
+                                ""actions"": [""read""]
+                            }
+                        ]
+                    }
+                }
+            }";
+
+            UpdateOptions options = new(
+                source: null,
+                permissions: null,
+                entity: "MyEntity",
+                sourceType: null,
+                sourceParameters: null,
+                sourceKeyFields: null,
+                restRoute: null,
+                graphQLType: null,
+                fieldsToInclude: null,
+                fieldsToExclude: null,
+                policyRequest: null,
+                policyDatabase: null,
+                relationship: null,
+                cardinality: null,
+                targetEntity: null,
+                linkingObject: null,
+                linkingSourceFields: null,
+                linkingTargetFields: null,
+                relationshipFields: null,
+                map: null,
+                cacheEnabled: null,
+                cacheTtl: null,
+                config: TEST_RUNTIME_CONFIG_FILE,
+                restMethodsForStoredProcedure: null,
+                graphQLOperationForStoredProcedure: null,
+                description: null,
+                parametersNameCollection: null,
+                parametersDescriptionCollection: null,
+                parametersRequiredCollection: null,
+                parametersDefaultCollection: null,
+                fieldsNameCollection: new[] { "Id" },
+                fieldsAliasCollection: null,
+                fieldsDescriptionCollection: new[] { "Unique Key" },
+                fieldsPrimaryKeyCollection: null,
+                mcpDmlTools: null,
+                mcpCustomTool: null
+            );
+
+            Assert.IsTrue(RuntimeConfigLoader.TryParseConfig(initialConfig, out RuntimeConfig? runtimeConfig), "Parsed config file.");
+            Assert.IsTrue(TryUpdateExistingEntity(options, runtimeConfig!, out RuntimeConfig updatedRuntimeConfig), "Successfully updated entity in the config.");
+
+            Entity updatedEntity = updatedRuntimeConfig.Entities["MyEntity"];
+            Assert.IsNotNull(updatedEntity.Fields);
+            Assert.AreEqual(1, updatedEntity.Fields!.Count);
+            FieldMetadata field = updatedEntity.Fields[0];
+            Assert.AreEqual("Id", field.Name);
+            Assert.AreEqual("Unique Key", field.Description);
+            Assert.IsTrue(field.PrimaryKey, "Primary key flag should be preserved when --fields.primary-key is not provided.");
+        }
+
         private static string GetInitialConfigString()
         {
             return @"{" +
diff --git a/src/Cli/ConfigGenerator.cs b/src/Cli/ConfigGenerator.cs
index 648edc1950..4e5b72b2c2 100644
--- a/src/Cli/ConfigGenerator.cs
+++ b/src/Cli/ConfigGenerator.cs
@@ -1747,6 +1747,7 @@ public static bool TryUpdateExistingEntity(UpdateOptions options, RuntimeConfig
                 List<FieldMetadata> updatedFieldsList = ComposeFieldsFromOptions(options);
                 Dictionary<string, FieldMetadata> updatedFieldsDict = updatedFieldsList.ToDictionary(f => f.Name, f => f);
                 List<FieldMetadata> mergedFields = [];
+                bool primaryKeyOptionProvided = options.FieldsPrimaryKeyCollection?.Any() == true;
 
                 foreach (FieldMetadata field in existingFields)
                 {
@@ -1757,7 +1758,10 @@ public static bool TryUpdateExistingEntity(UpdateOptions options, RuntimeConfig
                             Name = updatedField.Name,
                             Alias = updatedField.Alias ?? field.Alias,
                             Description = updatedField.Description ?? field.Description,
-                            PrimaryKey = updatedField.PrimaryKey
+                            // If --fields.primary-key was not provided at all,
+                            // keep the existing primary-key flag. Otherwise,
+                            // use the value coming from updatedField.
+                            PrimaryKey = primaryKeyOptionProvided ? updatedField.PrimaryKey : field.PrimaryKey
                         });
                         updatedFieldsDict.Remove(field.Name); // Remove so only new fields remain
                     }