diff --git a/apps/server-nestjs/src/modules/argocd/argocd-datastore.service.ts b/apps/server-nestjs/src/modules/argocd/argocd-datastore.service.ts
index d3103a2e3..efbf280d0 100644
--- a/apps/server-nestjs/src/modules/argocd/argocd-datastore.service.ts
+++ b/apps/server-nestjs/src/modules/argocd/argocd-datastore.service.ts
@@ -101,4 +101,11 @@ export class ArgoCDDatastoreService {
       select: projectSelect,
     })
   }
+
+  async getAllZoneSlugs(): Promise<string[]> {
+    const zones = await this.prisma.zone.findMany({
+      select: { slug: true },
+    })
+    return zones.map(zone => zone.slug)
+  }
 }
diff --git a/apps/server-nestjs/src/modules/argocd/argocd.service.spec.ts b/apps/server-nestjs/src/modules/argocd/argocd.service.spec.ts
index 95266ad47..cc41c30cc 100644
--- a/apps/server-nestjs/src/modules/argocd/argocd.service.spec.ts
+++ b/apps/server-nestjs/src/modules/argocd/argocd.service.spec.ts
@@ -34,6 +34,8 @@ describe('argoCDService', () => {
       deployVaultConnectionInNamespaces: false,
     })
 
+    datastore.getAllZoneSlugs.mockResolvedValue(['zone-1'])
+
     const module = await Test.createTestingModule({
       providers: [
         ArgoCDService,
@@ -352,6 +354,53 @@ describe('argoCDService', () => {
     expect(gitlab.generateCreateOrUpdateAction).toHaveBeenCalledTimes(1)
   })
 
+  it('should delete leftover values files when the project has no environments', async () => {
+    const mockProject = makeProjectWithDetails({
+      slug: 'project-1',
+      name: 'Project 1',
+      environments: [],
+      repositories: [makeProjectRepository({ internalRepoName: 'infra-repo', isInfra: true })],
+      deployments: [],
+    })
+
+    const infraProject = makeProjectSchema({ id: 100, http_url_to_repo: 'https://gitlab.internal/infra' })
+    datastore.getAllProjects.mockResolvedValue([mockProject])
+    // The project no longer has any environment, so the zone must be discovered
+    // from the platform zone list rather than from the project's environments.
+    datastore.getAllZoneSlugs.mockResolvedValue(['zone-1'])
+    gitlab.getOrCreateInfraGroupRepo.mockResolvedValue(infraProject)
+    gitlab.getOrCreateProjectGroupPublicUrl.mockResolvedValue('https://gitlab.internal/group')
+    gitlab.getOrCreateInfraGroupRepoPublicUrl.mockResolvedValue('https://gitlab.internal/infra-repo')
+    gitlab.listFiles.mockResolvedValue([
+      makeRepositoryTreeSchema(
+        { name: 'values.yaml', path: 'Project 1/cluster-1/dev/values.yaml' },
+      ),
+      makeRepositoryTreeSchema(
+        { name: 'values.yaml', path: 'Project 1/cluster-1/prod/values.yaml' },
+      ),
+    ])
+
+    await expect(service.handleCron()).resolves.not.toThrow()
+
+    expect(gitlab.maybeCreateCommit).toHaveBeenCalledTimes(1)
+    expect(gitlab.maybeCreateCommit).toHaveBeenCalledWith(
+      infraProject,
+      'ci: :robot_face: Sync project-1',
+      expect.arrayContaining([
+        {
+          action: 'delete',
+          filePath: 'Project 1/cluster-1/dev/values.yaml',
+        },
+        {
+          action: 'delete',
+          filePath: 'Project 1/cluster-1/prod/values.yaml',
+        },
+      ]),
+    )
+
+    expect(gitlab.generateCreateOrUpdateAction).not.toHaveBeenCalled()
+  })
+
   it('should not commit when there is no diff', async () => {
     const mockProject = makeProjectWithDetails({
       slug: 'project-1',
diff --git a/apps/server-nestjs/src/modules/argocd/argocd.service.ts b/apps/server-nestjs/src/modules/argocd/argocd.service.ts
index 7cd254fda..4d98330d7 100644
--- a/apps/server-nestjs/src/modules/argocd/argocd.service.ts
+++ b/apps/server-nestjs/src/modules/argocd/argocd.service.ts
@@ -101,7 +101,9 @@ export class ArgoCDService {
   ): Promise<void> {
     const span = trace.getActiveSpan()
     span?.setAttribute('project.slug', project.slug)
-    const zones = getDistinctZones(project)
+    // Visit every zone, not only those with a current environment, so leftover
+    // values files are purged from zones the project no longer deploys to.
+    const zones = await this.argoCDDatastore.getAllZoneSlugs()
     span?.setAttribute('argocd.zones.count', zones.length)
     this.logger.verbose(`Reconciling ArgoCD zones for project ${project.slug} (count=${zones.length})`)
     await Promise.all(zones.map(zoneSlug => this.ensureZone(project, zoneSlug)))
@@ -167,11 +169,6 @@ export class ArgoCDService {
     zoneSlug: string,
   ): Promise<CommitAction[]> {
     const neededFiles = new Set<string>()
-    const clusterLabelsInZone = new Set(
-      project.environments
-        .filter(e => e.cluster.zone.slug === zoneSlug)
-        .map(e => e.cluster.label),
-    )
 
     project.environments.forEach((env) => {
       if (env.cluster?.zone.slug !== zoneSlug) return
@@ -189,10 +186,6 @@ export class ArgoCDService {
         if (existingFile.name !== 'values.yaml') return false
         if (!existingFile.path.startsWith(projectPrefix)) return false
 
-        const remaining = existingFile.path.slice(projectPrefix.length)
-        const clusterLabel = remaining.split('/')[0]
-        if (!clusterLabel || !clusterLabelsInZone.has(clusterLabel)) return false
-
         return !neededFiles.has(existingFile.path)
       })
       .map(existingFile => ({ action: 'delete', filePath: existingFile.path } satisfies CommitAction))
@@ -445,12 +438,6 @@ function formatEnvironmentValuesFilePath(project: { name: string }, cluster: { l
   return `${project.name}/${cluster.label}/${env.name}/values.yaml`
 }
 
-function getDistinctZones(project: ProjectWithDetails) {
-  const zones = new Set<string>()
-  project.environments.forEach(e => zones.add(e.cluster.zone.slug))
-  return [...zones]
-}
-
 function splitExtraRepositories(extraRepositories: string | undefined): string[] {
   if (!extraRepositories) return []
   return extraRepositories.split(',').map(r => r.trim()).filter(r => r.length > 0)