diff --git a/packages/bruno-app/src/components/EnvironmentVariablesTable/index.js b/packages/bruno-app/src/components/EnvironmentVariablesTable/index.js
index f0fe61904..c1f05712a 100644
--- a/packages/bruno-app/src/components/EnvironmentVariablesTable/index.js
+++ b/packages/bruno-app/src/components/EnvironmentVariablesTable/index.js
@@ -495,7 +495,14 @@ const EnvironmentVariablesTable = ({
                     placeholder={isLastEmptyRow ? 'Value' : ''}
                     isSecret={variable.secret}
                     readOnly={typeof variable.value !== 'string'}
-                    onChange={(newValue) => formik.setFieldValue(`${actualIndex}.value`, newValue, true)}
+                    onChange={(newValue) => {
+                      formik.setFieldValue(`${actualIndex}.value`, newValue, true);
+                      // Clear ephemeral metadata when user manually edits the value
+                      if (variable.ephemeral) {
+                        formik.setFieldValue(`${actualIndex}.ephemeral`, undefined, false);
+                        formik.setFieldValue(`${actualIndex}.persistedValue`, undefined, false);
+                      }
+                    }}
                     onSave={handleSave}
                   />
                 </div>
diff --git a/packages/bruno-app/src/providers/ReduxStore/slices/collections/actions.js b/packages/bruno-app/src/providers/ReduxStore/slices/collections/actions.js
index fdadf4746..2a048b008 100644
--- a/packages/bruno-app/src/providers/ReduxStore/slices/collections/actions.js
+++ b/packages/bruno-app/src/providers/ReduxStore/slices/collections/actions.js
@@ -2063,7 +2063,14 @@ export const updateVariableInScope = (variableName, newValue, scopeInfo, collect
             return reject(new Error('Variable not found'));
           }
 
-          const updatedVariables = environment.variables.map((v) => (v.uid === variable.uid ? { ...v, value: newValue } : v));
+          const updatedVariables = environment.variables.map((v) => {
+            if (v.uid === variable.uid) {
+              // Clear ephemeral metadata when user manually edits the value
+              const { ephemeral, persistedValue, ...rest } = v;
+              return { ...rest, value: newValue };
+            }
+            return v;
+          });
 
           return dispatch(saveEnvironment(updatedVariables, environment.uid, collectionUid))
             .then(() => {
@@ -2172,8 +2179,14 @@ export const updateVariableInScope = (variableName, newValue, scopeInfo, collect
             return reject(new Error('Variable not found'));
           }
 
-          const updatedVariables = environment.variables.map((v) =>
-            v.uid === variable.uid ? { ...v, value: newValue } : v);
+          const updatedVariables = environment.variables.map((v) => {
+            if (v.uid === variable.uid) {
+              // Clear ephemeral metadata when user manually edits the value
+              const { ephemeral, persistedValue, ...rest } = v;
+              return { ...rest, value: newValue };
+            }
+            return v;
+          });
 
           return dispatch(saveGlobalEnvironment({ variables: updatedVariables, environmentUid: activeGlobalEnvUid }))
             .then(() => {