diff --git a/tests/System/integration/plugins/system/sef/SefPlugin.cy.js b/tests/System/integration/plugins/system/sef/SefPlugin.cy.js
index 35b27448284b0..b4a81da32df4e 100644
--- a/tests/System/integration/plugins/system/sef/SefPlugin.cy.js
+++ b/tests/System/integration/plugins/system/sef/SefPlugin.cy.js
@@ -1,77 +1,99 @@
 describe('Test that the sef system plugin', () => {
-  afterEach(() => {
-    cy.task('deleteRelativePath', '.htaccess');
-    cy.exec(`php ${Cypress.env('cmsPath')}/cli/joomla.php config:set sef=true sef_suffix=false sef_rewrite=false`);
-    cy.db_updateExtensionParameter('enforcesuffix', '1', 'plg_system_sef');
-    cy.db_updateExtensionParameter('indexphp', '1', 'plg_system_sef');
-    cy.db_updateExtensionParameter('trailingslash', '0', 'plg_system_sef');
-    cy.db_updateExtensionParameter('strictrouting', '1', 'plg_system_sef');
-  });
+  const setSefDefaults = () => cy.task('deleteRelativePath', '.htaccess')
+    .then(() => cy.config_setParameter('sef', true))
+    .then(() => cy.config_setParameter('sef_suffix', false))
+    .then(() => cy.config_setParameter('sef_rewrite', false))
+    .then(() => cy.db_updateExtensionParameter('enforcesuffix', '1', 'plg_system_sef'))
+    .then(() => cy.db_updateExtensionParameter('indexphp', '1', 'plg_system_sef'))
+    .then(() => cy.db_updateExtensionParameter('trailingslash', '0', 'plg_system_sef'))
+    .then(() => cy.db_updateExtensionParameter('strictrouting', '1', 'plg_system_sef'));
+
+  // Ensure that we always start with a clean SEF default state
+  beforeEach(() => setSefDefaults());
+
+  // Return to the clean SEF default state for subsequent Joomla System Tests
+  afterEach(() => setSefDefaults());
 
   it('can process if option \'sef\' disabled', () => {
-    cy.exec(`php ${Cypress.env('cmsPath')}/cli/joomla.php config:set sef=false`);
-    cy.request({ url: '/index.php?option=com_users&view=login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
-    cy.request({ url: '/index.php/component/users/login', failOnStatusCode: false, followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(404);
-    });
+    cy.config_setParameter('sef', false)
+      .then(() => {
+        cy.request({ url: '/index.php?option=com_users&view=login', followRedirect: false })
+          .then((response) => {
+            expect(response.status).to.eq(200);
+          });
+        cy.request({ url: '/index.php/component/users/login', failOnStatusCode: false, followRedirect: false })
+          .then((response) => {
+            expect(response.status).to.eq(404);
+          });
+      });
   });
 
   it('can process if option \'enforcesuffix\' enabled', () => {
-    cy.exec(`php ${Cypress.env('cmsPath')}/cli/joomla.php config:set sef_suffix=true`);
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(301);
-      expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login\.html$/);
-    });
-    cy.request({ url: '/index.php/component/users/login.html', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.config_setParameter('sef_suffix', true)
+      .then(() => {
+        cy.request({ url: '/index.php/component/users/login', followRedirect: false })
+          .then((response) => {
+            expect(response.status).to.eq(301);
+            expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login\.html$/);
+          });
+        cy.request({ url: '/index.php/component/users/login.html', followRedirect: false })
+          .then((response) => {
+            expect(response.status).to.eq(200);
+          });
+      });
   });
 
   it('can process if option \'enforcesuffix\' disabled', () => {
-    cy.exec(`php ${Cypress.env('cmsPath')}/cli/joomla.php config:set sef_suffix=true`);
-    cy.db_updateExtensionParameter('enforcesuffix', '0', 'plg_system_sef');
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
-    cy.request({ url: '/index.php/component/users/login.html', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.config_setParameter('sef_suffix', true)
+      .then(() => cy.db_updateExtensionParameter('enforcesuffix', '0', 'plg_system_sef'))
+      .then(() => cy.request({ url: '/index.php/component/users/login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      })
+      .then(() => cy.request({ url: '/index.php/component/users/login.html', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      });
   });
 
   it('can process if option \'indexphp\' enabled', () => {
-    cy.exec(`php ${Cypress.env('cmsPath')}/cli/joomla.php config:set sef_rewrite=true`);
-    cy.task('copyRelativeFile', { source: 'htaccess.txt', destination: '.htaccess' });
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(301);
-      expect(response.redirectedToUrl).to.match(/(?<!index\.php)\/component\/users\/login$/);
-    });
-    cy.request({ url: '/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.config_setParameter('sef_rewrite', true)
+      .then(() => cy.task('copyRelativeFile', { source: 'htaccess.txt', destination: '.htaccess' }))
+      .then(() => cy.request({ url: '/index.php/component/users/login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(301);
+        expect(response.redirectedToUrl).to.match(/(?<!index\.php)\/component\/users\/login$/);
+      })
+      .then(() => cy.request({ url: '/component/users/login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      });
   });
 
   it('can process if option \'indexphp\' disabled', () => {
-    cy.exec(`php ${Cypress.env('cmsPath')}/cli/joomla.php config:set sef_rewrite=true`);
-    cy.task('copyRelativeFile', { source: 'htaccess.txt', destination: '.htaccess' });
-    cy.db_updateExtensionParameter('indexphp', '0', 'plg_system_sef');
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
-    cy.request({ url: '/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.config_setParameter('sef_rewrite', true)
+      .then(() => cy.task('copyRelativeFile', { source: 'htaccess.txt', destination: '.htaccess' }))
+      .then(() => cy.db_updateExtensionParameter('indexphp', '0', 'plg_system_sef'))
+      .then(() => cy.request({ url: '/index.php/component/users/login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      })
+      .then(() => cy.request({ url: '/component/users/login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      });
   });
 
   it('can process if option \'trailingslash\' disabled', () => {
-    cy.request({ url: '/index.php/component/users/login/', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(301);
-      expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login$/);
-    });
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.request({ url: '/index.php/component/users/login/', followRedirect: false })
+      .then((response) => {
+        expect(response.status).to.eq(301);
+        expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login$/);
+      });
+    cy.request({ url: '/index.php/component/users/login', followRedirect: false })
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      });
     cy.visit('/');
     cy.get('li.nav-item').contains('Home')
       .should('have.attr', 'href')
@@ -79,14 +101,16 @@ describe('Test that the sef system plugin', () => {
   });
 
   it('can process if option \'trailingslash\' enabled', () => {
-    cy.db_updateExtensionParameter('trailingslash', '1', 'plg_system_sef');
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(301);
-      expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login\/$/);
-    });
-    cy.request({ url: '/index.php/component/users/login/', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.db_updateExtensionParameter('trailingslash', '1', 'plg_system_sef')
+      .then(() => cy.request({ url: '/index.php/component/users/login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(301);
+        expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login\/$/);
+      })
+      .then(() => cy.request({ url: '/index.php/component/users/login/', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      });
     cy.visit('/');
     cy.get('li.nav-item').contains('Home')
       .should('have.attr', 'href')
@@ -94,22 +118,26 @@ describe('Test that the sef system plugin', () => {
   });
 
   it('can process if option \'strictrouting\' enabled', () => {
-    cy.request({ url: '/index.php?option=com_users&view=login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(301);
-      expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login$/);
-    });
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.request({ url: '/index.php?option=com_users&view=login', followRedirect: false })
+      .then((response) => {
+        expect(response.status).to.eq(301);
+        expect(response.redirectedToUrl).to.match(/\/index\.php\/component\/users\/login$/);
+      });
+    cy.request({ url: '/index.php/component/users/login', followRedirect: false })
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      });
   });
 
   it('can process if option \'strictrouting\' disabled', () => {
-    cy.db_updateExtensionParameter('strictrouting', '0', 'plg_system_sef');
-    cy.request({ url: '/index.php?option=com_users&view=login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
-    cy.request({ url: '/index.php/component/users/login', followRedirect: false }).then((response) => {
-      expect(response.status).to.eq(200);
-    });
+    cy.db_updateExtensionParameter('strictrouting', '0', 'plg_system_sef')
+      .then(() => cy.request({ url: '/index.php?option=com_users&view=login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      })
+      .then(() => cy.request({ url: '/index.php/component/users/login', followRedirect: false }))
+      .then((response) => {
+        expect(response.status).to.eq(200);
+      });
   });
 });
diff --git a/tests/System/plugins/fs.mjs b/tests/System/plugins/fs.mjs
index 5dd1a23e3a59c..9bbd65be11321 100644
--- a/tests/System/plugins/fs.mjs
+++ b/tests/System/plugins/fs.mjs
@@ -36,24 +36,29 @@ function deleteRelativePath(relativePath, config) {
  * @returns null
  */
 function writeRelativeFile(relativePath, content, config, mode = 0o444) {
-  const fullPath = join(config.env.cmsPath, relativePath);
-  // Prologue: Reset process file mode creation mask to ensure the umask value is not subtracted
-  const oldmask = umask(0);
-  // Create missing parent directories with 'rwxrwxrwx'
-  mkdirSync(dirname(fullPath), { recursive: true, mode: 0o777 });
-  // Check if the file exists
-  if (existsSync(fullPath)) {
-    // Set 'rw-rw-rw-' to be able to overwrite the file
-    chmodSync(fullPath, 0o666);
-  }
-  // Write or overwrite the file on relative path with given content
-  writeFileSync(fullPath, content);
-  // Finally set given file mode or default 'r--r--r--'
-  chmodSync(fullPath, mode);
-  // Epilogue: Restore process file mode creation mask
-  umask(oldmask);
-
-  return null;
+  return new Promise((resolve, reject) => {
+    try {
+      const fullPath = join(config.env.cmsPath, relativePath);
+      // Prologue: Reset process file mode creation mask to ensure the umask value is not subtracted
+      const oldmask = umask(0);
+      // Create missing parent directories with 'rwxrwxrwx'
+      mkdirSync(dirname(fullPath), { recursive: true, mode: 0o777 });
+      // Check if the file exists
+      if (existsSync(fullPath)) {
+        // Set 'rw-rw-rw-' to be able to overwrite the file
+        chmodSync(fullPath, 0o666);
+      }
+      // Write or overwrite the file on relative path with given content
+      writeFileSync(fullPath, content);
+      // Finally set given file mode or default 'r--r--r--'
+      chmodSync(fullPath, mode);
+      // Epilogue: Restore process file mode creation mask
+      umask(oldmask);
+      resolve(`File successfully written: ${fullPath}`);
+    } catch (error) {
+      reject(new Error(`Failed to write file: ${error.message}`));
+    }
+  });
 }
 
 /**
diff --git a/tests/System/support/commands/config.mjs b/tests/System/support/commands/config.mjs
index 4987273e8ee49..b044974663cae 100644
--- a/tests/System/support/commands/config.mjs
+++ b/tests/System/support/commands/config.mjs
@@ -1,7 +1,8 @@
 Cypress.Commands.add('config_setParameter', (parameter, value) => {
   const configPath = `${Cypress.env('cmsPath')}/configuration.php`;
 
-  cy.readFile(configPath).then((fileContent) => {
+  // Return a Cypress chainable for chaining
+  return cy.readFile(configPath).then((fileContent) => {
     // Setup the new value
     const newValue = typeof value === 'string' ? `'${value}'` : value;
 
@@ -11,7 +12,11 @@ Cypress.Commands.add('config_setParameter', (parameter, value) => {
     // Replace the whole line with the new value
     const content = fileContent.replace(regex, `public $${parameter} = ${newValue};`);
 
-    // Write the modified content back to the configuration file relative to the CMS root folder
-    cy.task('writeRelativeFile', { path: 'configuration.php', content });
+    /* Write the modified content back to the configuration file relative to the CMS root folder and
+     * wait for the task to complete and chain it.
+     */
+    return cy.task('writeRelativeFile', { path: 'configuration.php', content }).then((result) => {
+      cy.log(result); // Log success message for debugging
+    });
   });
 });