diff --git a/test/e2e/config/e2e.json b/test/e2e/config/e2e.json
index ac19a1a09..453ca92a6 100644
--- a/test/e2e/config/e2e.json
+++ b/test/e2e/config/e2e.json
@@ -1,6 +1,10 @@
 {
   "timeouts": {
     "defaultCommandTimeout": 20000,
-    "pageLoadTimeout": 45000
+    "pageLoadTimeout": 45000,
+    "webviewLoad": 30000,
+    "deployment": 60000,
+    "oauthFlow": 90000,
+    "apiRequest": 10000
   }
 }
diff --git a/test/e2e/cypress.config.js b/test/e2e/cypress.config.js
index 2a41b6eeb..71756d047 100644
--- a/test/e2e/cypress.config.js
+++ b/test/e2e/cypress.config.js
@@ -32,7 +32,7 @@ module.exports = defineConfig({
     supportFile: "support/index.js",
     specPattern: "tests/**/*.cy.{js,jsx,ts,tsx}",
     retries: {
-      runMode: 2, // Retry failed tests in run mode (CI)
+      runMode: 3, // Retry failed tests in run mode (CI) - increased from 2 for stability
       openMode: 0,
     },
     defaultCommandTimeout: e2eConfig.timeouts.defaultCommandTimeout,
diff --git a/test/e2e/support/commands.js b/test/e2e/support/commands.js
index 11b77fb76..9d632d6ba 100644
--- a/test/e2e/support/commands.js
+++ b/test/e2e/support/commands.js
@@ -8,10 +8,43 @@ import "./selectors";
 import "./sequences";
 import "./workbench";
 
+// verifyServicesReady: Check that all required services are responding before tests
+// This prevents flaky failures due to services not being fully ready
+Cypress.Commands.add("verifyServicesReady", () => {
+  const connectUrl =
+    Cypress.env("CONNECT_SERVER_URL") || "http://localhost:3939";
+  const baseUrl = Cypress.config("baseUrl");
+
+  // Verify Connect server is responding
+  cy.request({
+    url: `${connectUrl}/__ping__`,
+    retryOnStatusCodeFailure: true,
+    timeout: 30000,
+    failOnStatusCode: false,
+  }).then((response) => {
+    if (response.status !== 200) {
+      cy.log(`WARNING: Connect server returned status ${response.status}`);
+    }
+  });
+
+  // Verify code-server is responding
+  cy.request({
+    url: baseUrl,
+    retryOnStatusCodeFailure: true,
+    timeout: 30000,
+    failOnStatusCode: false,
+  }).then((response) => {
+    if (response.status !== 200) {
+      cy.log(`WARNING: code-server returned status ${response.status}`);
+    }
+  });
+});
+
 // initializeConnect: Simple initialization for use with with-connect action
 // The API key is passed via CYPRESS_BOOTSTRAP_ADMIN_API_KEY environment variable
 // from the with-connect GitHub Action, which handles Connect startup and bootstrapping.
 Cypress.Commands.add("initializeConnect", () => {
+  cy.verifyServicesReady();
   cy.clearupDeployments();
   cy.setAdminCredentials();
 });
@@ -456,12 +489,15 @@ Cypress.Commands.add(
         if (result && result.length) {
           return result;
         } else if (attempt < maxAttempts) {
-          // Cap max delay at 5 seconds to prevent exponential backoff from causing very long waits
-          const delay = Math.min(initialDelay * Math.pow(2, attempt - 1), 5000);
+          // Cap max delay at 3 seconds to prevent exponential backoff from causing very long waits
+          const delay = Math.min(initialDelay * Math.pow(2, attempt - 1), 3000);
+
           cy.wait(delay);
           return tryFn();
         } else {
-          throw new Error("Element not found after retries with backoff");
+          throw new Error(
+            `Element not found after ${maxAttempts} retries with backoff`,
+          );
         }
       });
     }
diff --git a/test/e2e/support/selectors.js b/test/e2e/support/selectors.js
index d68f2d8fe..c93b72bb8 100644
--- a/test/e2e/support/selectors.js
+++ b/test/e2e/support/selectors.js
@@ -274,6 +274,10 @@ Cypress.Commands.add("toggleCredentialsSection", () => {
 });
 
 Cypress.Commands.add("refreshCredentials", () => {
+  // Intercept the credentials API call before triggering refresh
+  // Match both /api/credentials and /credentials endpoints
+  cy.intercept("GET", "**/credentials**").as("credentialsRefresh");
+
   // Robustly locate the credentials section inside the webview before interacting
   cy.retryWithBackoff(
     () =>
@@ -297,8 +301,17 @@ Cypress.Commands.add("refreshCredentials", () => {
     }
   });
 
-  // Wait for credential refresh API call to complete
-  cy.waitForNetworkIdle(500);
+  // Wait for credential refresh API call to complete, with additional network idle as backup
+  cy.wait("@credentialsRefresh", { timeout: 10000 }).then((interception) => {
+    if (interception.response?.statusCode !== 200) {
+      cy.log(
+        `Credentials refresh returned status: ${interception.response?.statusCode}`,
+      );
+    }
+  });
+
+  // Additional brief wait for UI to update after API response
+  cy.waitForNetworkIdle(200);
 });
 
 Cypress.Commands.add("toggleHelpSection", () => {
diff --git a/test/e2e/support/sequences.js b/test/e2e/support/sequences.js
index 0c16db06e..171ff98d4 100644
--- a/test/e2e/support/sequences.js
+++ b/test/e2e/support/sequences.js
@@ -323,9 +323,7 @@ Cypress.Commands.add(
             const isChecked = $checkbox.prop("checked");
             if (!isChecked) {
               cy.wrap($checkbox).click({ force: true });
-              // eslint-disable-next-line cypress/no-unnecessary-waiting
-              cy.wait(500); // Small wait after click
-              // Verify the click worked
+              // Verify the click worked - Cypress will retry until checked
               cy.wrap($checkbox).should("be.checked");
             }
           });
@@ -372,6 +370,10 @@ Cypress.Commands.add(
 // Purpose: Click the Deploy button, wait for toasts to clear, and confirm success.
 // When to use: Immediately after createPCSDeployment/createPCCDeployment when deployment should succeed.
 Cypress.Commands.add("deployCurrentlySelected", () => {
+  // Intercept deploy API calls for better synchronization
+  cy.intercept("POST", "**/api/publish/**").as("publishRequest");
+  cy.intercept("GET", "**/api/deployments/**").as("deploymentsCheck");
+
   // Wait for any pending network activity to settle before deploying
   cy.waitForNetworkIdle(500);
 
@@ -381,6 +383,10 @@ Cypress.Commands.add("deployCurrentlySelected", () => {
     .then((dplyBtn) => {
       Cypress.$(dplyBtn).trigger("click");
     });
+
+  // Wait for the publish request to start
+  cy.wait("@publishRequest", { timeout: 30000 });
+
   // Wait for deploying message to finish
   cy.get(".notifications-toasts", { timeout: 30_000 })
     .should("be.visible")
@@ -500,10 +506,12 @@ Cypress.Commands.add("startCredentialCreationFlow", (platform = "server") => {
             })`,
           );
           $sec.find(".title").trigger("click");
-          // eslint-disable-next-line cypress/no-unnecessary-waiting
-          cy.wait(200).then(() =>
-            ensureCredentialsSectionExpanded(attempt + 1),
-          );
+          // Wait for the section to expand by checking for visible content
+          cy.publisherWebview()
+            .findByTestId("publisher-credentials-section")
+            .find(".pane-body, .tree, :contains('No credentials')")
+            .should("be.visible")
+            .then(() => ensureCredentialsSectionExpanded(attempt + 1));
         } else {
           cy.log("Credentials section expanded");
         }
diff --git a/test/e2e/support/workbench.js b/test/e2e/support/workbench.js
index af059c624..9bc8ea2ae 100644
--- a/test/e2e/support/workbench.js
+++ b/test/e2e/support/workbench.js
@@ -243,13 +243,13 @@ Cypress.Commands.add("startPositronSession", () => {
 
   // Start a Positron session
   // TODO remove this workaround for "All types of sessions are disabled" error after Workbench 2025.12.0 is released
+  // Wait for the button to be fully interactive before clicking
   cy.get("button")
     .contains("New Session")
     .should("be.visible")
-    .and("be.enabled");
-  // eslint-disable-next-line cypress/no-unnecessary-waiting
-  cy.wait(500);
-  cy.get("button").contains("New Session").click();
+    .and("be.enabled")
+    .and("not.have.attr", "aria-busy", "true")
+    .click();
   cy.get("button").contains("Positron").click();
   cy.get("button").contains("Launch").click();