diff --git a/cypress/tests/data/10-ApplicationSetup/20-CreateContext.cy.js b/cypress/tests/data/10-ApplicationSetup/20-CreateContext.cy.js
index dde4dc4eca..ff8fba89f1 100644
--- a/cypress/tests/data/10-ApplicationSetup/20-CreateContext.cy.js
+++ b/cypress/tests/data/10-ApplicationSetup/20-CreateContext.cy.js
@@ -60,7 +60,7 @@ describe('Data suite tests', function() {
 		cy.login('admin', 'admin');
 		cy.get('a').contains('admin').click();
 		cy.get('a').contains('Dashboard').click();
-		cy.get('.app__nav a').contains('Administration').click();
+		cy.get('nav').contains('Administration').click();
 		cy.get('a').contains('Hosted Servers').click();
 		cy.get('a[class=show_extras]').click();
 		cy.contains('Settings wizard').click();
@@ -99,7 +99,9 @@ describe('Data suite tests', function() {
 		cy.login('admin', 'admin');
 		cy.get('a').contains('admin').click();
 		cy.get('a').contains('Dashboard').click();
-		cy.get('.app__nav a').contains('Server').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Server').click({ force: true });
 
 		cy.get('input[name="abbreviation-en"]').type('Pub Know Pre', {delay: 0});
 		cy.get('input[name="acronym-en"]').type(Cypress.env('contextAcronyms')['en'], {delay: 0});
@@ -112,7 +114,9 @@ describe('Data suite tests', function() {
 		cy.login('admin', 'admin');
 		cy.get('a').contains('admin').click();
 		cy.get('a').contains('Dashboard').click();
-		cy.get('.app__nav a').contains('Server').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Server').click({ force: true });
 		cy.get('button[id="contact-button"]').click();
 
 		// Submit the form with required fields missing.
diff --git a/cypress/tests/data/10-ApplicationSetup/40-CreateUsers.cy.js b/cypress/tests/data/10-ApplicationSetup/40-CreateUsers.cy.js
index 2a727c52a1..2737c53caa 100644
--- a/cypress/tests/data/10-ApplicationSetup/40-CreateUsers.cy.js
+++ b/cypress/tests/data/10-ApplicationSetup/40-CreateUsers.cy.js
@@ -12,7 +12,9 @@ describe('Data suite tests', function() {
 		cy.login('admin', 'admin');
 		cy.get('a:contains("admin"):visible').click();
 		cy.get('a:contains("Dashboard")').click();
-		cy.get('a:contains("Users & Roles")').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Users & Roles').click({ force: true });
 
 		var users = [
 			{
diff --git a/cypress/tests/data/10-ApplicationSetup/50-SubmissionGroups.cy.js b/cypress/tests/data/10-ApplicationSetup/50-SubmissionGroups.cy.js
index f9d91fd550..27da72a8d1 100644
--- a/cypress/tests/data/10-ApplicationSetup/50-SubmissionGroups.cy.js
+++ b/cypress/tests/data/10-ApplicationSetup/50-SubmissionGroups.cy.js
@@ -12,7 +12,9 @@ describe('Data suite tests', function() {
 		cy.login('admin', 'admin');
 		cy.get('a').contains('admin').click();
 		cy.get('a').contains('Dashboard').click();
-		cy.get('.app__nav a').contains('Server').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Server').click({ force: true });
 		cy.get('button[id="sections-button"]').click();
 
 		// Edit Preprints section to add section editors
@@ -28,7 +30,9 @@ describe('Data suite tests', function() {
 		cy.login('admin', 'admin');
 		cy.get('a').contains('admin').click();
 		cy.get('a').contains('Dashboard').click();
-		cy.get('.app__nav a').contains('Server').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Server').click({ force: true });
 		cy.get('button[id="categories-button"]').click();
 
 		cy.addCategory('History', 'history');
diff --git a/cypress/tests/integration/Doi.cy.js b/cypress/tests/integration/Doi.cy.js
index 6b50439402..231eb04e3d 100644
--- a/cypress/tests/integration/Doi.cy.js
+++ b/cypress/tests/integration/Doi.cy.js
@@ -15,7 +15,7 @@ describe('DOI tests', function() {
 
 	const loginAndGoToDoiPage = () => {
 		cy.login('dbarnes', null, 'publicknowledge');
-		cy.get('a:contains("DOIs")').click();
+		cy.get('nav').contains('DOIs').click();
 		cy.get('button#submission-doi-management-button').click();
 	};
 
@@ -291,7 +291,9 @@ describe('DOI tests', function() {
 		cy.log("Check DOI versioning off creates new DOI for first version");
 
 		// Turn DOI versioning off
-		cy.get('a:contains("Distribution")').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Distribution').click({ force: true });
 		cy.get('button#dois-button').click();
 
 		cy.get("input[name=doiVersioning][value=false]").click();
@@ -302,7 +304,7 @@ describe('DOI tests', function() {
 		cy.get('#doisSetup [role="status"]').contains('Saved');
 
 		//Go to publication and rollback to first publication being unpublished, then republish first publication
-		cy.get('a:contains("Submissions")').click();
+		cy.get('nav').contains('Submissions').click();
 		cy.get('button:contains("Archived")').click();
 		cy.get(`div#archive .listPanel__item:contains("${articleTitle}") a:contains("View")`).click();
 
@@ -347,7 +349,7 @@ describe('DOI tests', function() {
 		cy.log("Check DOI versioning off copies previous DOI for subsequent versions");
 
 		// Publish Version 2
-		cy.get('a:contains("Submissions")').click();
+		cy.get('nav').contains('Submissions').click();
 		cy.get('button:contains("Archived")').click();
 		cy.get(`div#archive .listPanel__item:contains("${articleTitle}") a:contains("View")`).click();
 		cy.get('button#publication-button').click();
@@ -400,7 +402,9 @@ describe('DOI tests', function() {
 			);
 
 		// Change DOI versioning to "on" to confirm DOI was copied properly
-		cy.get('a:contains("Distribution")').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Distribution').click({ force: true });
 		cy.get('button#dois-button').click();
 
 		cy.get("input[name=doiVersioning][value=true]").click();
@@ -483,7 +487,7 @@ describe('DOI tests', function() {
 
 		// Check creates new version
 		// Go to publication and publish Version 2
-		cy.get('a:contains("Submissions")').click();
+		cy.get('nav').contains('Submissions').click();
 		cy.get('button:contains("Archived")').click();
 		cy.get(`div#archive .listPanel__item:contains("${articleTitle}") a:contains("View")`).click();
 		cy.get('button#publication-button').click();
diff --git a/cypress/tests/integration/DoiCrossref.cy.js b/cypress/tests/integration/DoiCrossref.cy.js
index 10172c230d..bd3d6a08f1 100644
--- a/cypress/tests/integration/DoiCrossref.cy.js
+++ b/cypress/tests/integration/DoiCrossref.cy.js
@@ -13,7 +13,9 @@ describe('Crossref tests', function () {
 	it('Check Crossref Configuration', function() {
 		cy.login('dbarnes', null, 'publicknowledge');
 
-		cy.get('a:contains("Website")').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Website').click({ force: true });
 
 		cy.waitJQuery();
 		cy.get('button#plugins-button').click();
@@ -23,7 +25,9 @@ describe('Crossref tests', function () {
 		cy.get('input[id^=select-cell-crossrefplugin]').should('be.checked');
 
 		// Crossref is enabled as DOI registration agency.
-		cy.get('a:contains("Distribution")').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Distribution').click({ force: true });
 		cy.get('button#dois-button').click();
 		cy.get(
 			'#doiSetup input[name="enabledDoiTypes"][value="representation"]'
@@ -73,7 +77,9 @@ describe('Crossref tests', function () {
 			});
 
 		cy.log('Deselect Crossref as registered agency for downstream tests');
-		cy.get('a:contains("Distribution")').click();
+		cy.get('nav').contains('Settings').click();
+		// Ensure submenu item click despite animation
+		cy.get('nav').contains('Distribution').click({ force: true });
 		cy.get('button#dois-button').click();
 		cy.get('button#doisRegistration-button').click();
 		cy.get('select#doiRegistrationSettings-registrationAgency-control').select(