diff --git a/lib/commands/publish.js b/lib/commands/publish.js
index 0456fd7e8320e..cf6b50cce3c21 100644
--- a/lib/commands/publish.js
+++ b/lib/commands/publish.js
@@ -220,7 +220,12 @@ class Publish extends BaseCommand {
       })
     }
     if (manifest.publishConfig) {
-      flatten(manifest.publishConfig, opts)
+      const cliFlags = this.npm.config.data.get('cli').raw
+      // Filter out properties set in CLI flags to prioritize them over
+      // corresponding `publishConfig` settings
+      const filteredPublishConfig = Object.fromEntries(
+        Object.entries(manifest.publishConfig).filter(([key]) => !(key in cliFlags)))
+      flatten(filteredPublishConfig, opts)
     }
     return manifest
   }
diff --git a/lib/commands/unpublish.js b/lib/commands/unpublish.js
index a9c20900534c3..a4d445a035b62 100644
--- a/lib/commands/unpublish.js
+++ b/lib/commands/unpublish.js
@@ -141,7 +141,12 @@ class Unpublish extends BaseCommand {
     // If localPrefix has a package.json with a name that matches the package
     // being unpublished, load up the publishConfig
     if (manifest?.name === spec.name && manifest.publishConfig) {
-      flatten(manifest.publishConfig, opts)
+      const cliFlags = this.npm.config.data.get('cli').raw
+      // Filter out properties set in CLI flags to prioritize them over
+      // corresponding `publishConfig` settings
+      const filteredPublishConfig = Object.fromEntries(
+        Object.entries(manifest.publishConfig).filter(([key]) => !(key in cliFlags)))
+      flatten(filteredPublishConfig, opts)
     }
 
     const versions = await Unpublish.getKeysOfVersions(spec.name, opts)
diff --git a/tap-snapshots/test/lib/commands/publish.js.test.cjs b/tap-snapshots/test/lib/commands/publish.js.test.cjs
index 1bbdebb4fd617..eb2b021e5d8c8 100644
--- a/tap-snapshots/test/lib/commands/publish.js.test.cjs
+++ b/tap-snapshots/test/lib/commands/publish.js.test.cjs
@@ -452,6 +452,10 @@ exports[`test/lib/commands/publish.js TAP restricted access > new package versio
 + @npm/test-package@1.0.0
 `
 
+exports[`test/lib/commands/publish.js TAP prioritize CLI flags over publishConfig > new package version 1`] = `
++ test-package@1.0.0
+`
+
 exports[`test/lib/commands/publish.js TAP scoped _auth config scoped registry > new package version 1`] = `
 + @npm/test-package@1.0.0
 `
diff --git a/test/lib/commands/publish.js b/test/lib/commands/publish.js
index ec7299e9eec53..751cd97d8acf6 100644
--- a/test/lib/commands/publish.js
+++ b/test/lib/commands/publish.js
@@ -131,6 +131,58 @@ t.test('re-loads publishConfig.registry if added during script process', async t
   t.matchSnapshot(joinedOutput(), 'new package version')
 })
 
+t.test('prioritize CLI flags over publishConfig', async t => {
+  const publishConfig = { registry: 'http://publishconfig' }
+  const { joinedOutput, npm } = await loadMockNpm(t, {
+    config: {
+      [`${alternateRegistry.slice(6)}/:_authToken`]: 'test-other-token',
+    },
+    prefixDir: {
+      'package.json': JSON.stringify({
+        ...pkgJson,
+        scripts: {
+          prepare: 'cp new.json package.json',
+        },
+      }, null, 2),
+      'new.json': JSON.stringify({
+        ...pkgJson,
+        publishConfig,
+      }),
+    },
+    argv: ['--registry', alternateRegistry],
+  })
+  const registry = new MockRegistry({
+    tap: t,
+    registry: alternateRegistry,
+    authorization: 'test-other-token',
+  })
+  registry.nock.put(`/${pkg}`, body => {
+    return t.match(body, {
+      _id: pkg,
+      name: pkg,
+      'dist-tags': { latest: '1.0.0' },
+      access: null,
+      versions: {
+        '1.0.0': {
+          name: pkg,
+          version: '1.0.0',
+          _id: `${pkg}@1.0.0`,
+          dist: {
+            shasum: /\.*/,
+            tarball: `http:${alternateRegistry.slice(6)}/test-package/-/test-package-1.0.0.tgz`,
+          },
+          publishConfig,
+        },
+      },
+      _attachments: {
+        [`${pkg}-1.0.0.tgz`]: {},
+      },
+    })
+  }).reply(200, {})
+  await npm.exec('publish', [])
+  t.matchSnapshot(joinedOutput(), 'new package version')
+})
+
 t.test('json', async t => {
   const { joinedOutput, npm, logs } = await loadMockNpm(t, {
     config: {
diff --git a/test/lib/commands/unpublish.js b/test/lib/commands/unpublish.js
index 097309393a258..31dc77ea46cd0 100644
--- a/test/lib/commands/unpublish.js
+++ b/test/lib/commands/unpublish.js
@@ -408,6 +408,36 @@ t.test('publishConfig no spec', async t => {
   t.equal(joinedOutput(), '- test-package')
 })
 
+t.test('prioritize CLI flags over publishConfig no spec', async t => {
+  const alternateRegistry = 'https://other.registry.npmjs.org'
+  const publishConfig = { registry: 'http://publishconfig' }
+  const { joinedOutput, npm } = await loadMockNpm(t, {
+    config: {
+      force: true,
+      '//other.registry.npmjs.org/:_authToken': 'test-other-token',
+    },
+    prefixDir: {
+      'package.json': JSON.stringify({
+        name: pkg,
+        version: '1.0.0',
+        publishConfig,
+      }, null, 2),
+    },
+    argv: ['--registry', alternateRegistry],
+  })
+
+  const registry = new MockRegistry({
+    tap: t,
+    registry: alternateRegistry,
+    authorization: 'test-other-token',
+  })
+  const manifest = registry.manifest({ name: pkg })
+  await registry.package({ manifest, query: { write: true }, times: 2 })
+  registry.unpublish({ manifest })
+  await npm.exec('unpublish', [])
+  t.equal(joinedOutput(), '- test-package')
+})
+
 t.test('publishConfig with spec', async t => {
   const alternateRegistry = 'https://other.registry.npmjs.org'
   const { joinedOutput, npm } = await loadMockNpm(t, {