diff --git a/LICENSE.txt b/LICENSE.txt
index 6cfd87342..fa1e65c74 100644
--- a/LICENSE.txt
+++ b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2024, Salesforce.com, Inc.
+Copyright (c) 2025, Salesforce.com, Inc.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
diff --git a/README.md b/README.md
index 1deef4292..294072026 100644
--- a/README.md
+++ b/README.md
@@ -1282,8 +1282,9 @@ Create a project manifest that lists the metadata components you want to deploy
 
 ```
 USAGE
-  $ sf project generate manifest [--json] [--flags-dir <value>] [--api-version <value>] [-m <value>...] [-p <value>...] [-n
-    <value> | -t pre|post|destroy|package] [-c managed|unlocked... --from-org <value>] [-d <value>]
+  $ sf project generate manifest [--json] [--flags-dir <value>] [--api-version <value>] [-m <value>... | -p <value>...] [-n
+    <value> | -t pre|post|destroy|package] [-c managed|unlocked... --from-org <value>] [--excluded-metadata <value>... ]
+    [-d <value>]
 
 FLAGS
   -c, --include-packages=<option>...  Package types (managed, unlocked) whose metadata is included in the manifest; by
@@ -1297,6 +1298,8 @@ FLAGS
   -t, --type=<option>                 Type of manifest to create; the type determines the name of the created file.
                                       <options: pre|post|destroy|package>
       --api-version=<value>           Override the api version used for api requests made by this command
+      --excluded-metadata=<value>...  Metadata types to exclude when building a manifest from an org. Specify the name
+                                      of the type, not the name of a specific component.
       --from-org=<value>              Username or alias of the org that contains the metadata components from which to
                                       build a manifest.
 
@@ -1329,6 +1332,14 @@ DESCRIPTION
   multiple names separated by spaces. Enclose names that contain spaces in one set of double quotes. The same syntax
   applies to --include-packages and --source-dir.
 
+  To build a manifest from the metadata in an org, use the --from-org flag. You can combine --from-org with the
+  --metadata flag to include only certain metadata types, or with the --excluded-metadata flag to exclude certain
+  metadata types. When building a manifest from an org, the command makes many concurrent API calls to discover the
+  metadata that exists in the org. To limit the number of concurrent requests, use the SF_LIST_METADATA_BATCH_SIZE
+  environment variable and set it to a size that works best for your org and environment. If you experience timeouts or
+  inconsistent manifest contents, then setting this environment variable can improve accuracy. However, the command
+  takes longer to run because it sends fewer requests at a time.
+
 ALIASES
   $ sf force source manifest create
 
@@ -1349,6 +1360,14 @@ EXAMPLES
   Create a manifest from the metadata components in the specified org and include metadata in any unlocked packages:
 
     $ sf project generate manifest --from-org test@myorg.com --include-packages unlocked
+
+  Create a manifest from specific metadata types in an org:
+
+    $ sf project generate manifest --from-org test@myorg.com --metadata ApexClass,CustomObject,CustomLabels
+
+  Create a manifest from all metadata components in an org excluding specific metadata types:
+
+    $ sf project generate manifest --from-org test@myorg.com --excluded-metadata StandardValueSet
 ```
 
 _See code: [src/commands/project/generate/manifest.ts](https://github.com/salesforcecli/plugin-deploy-retrieve/blob/3.16.6/src/commands/project/generate/manifest.ts)_
diff --git a/command-snapshot.json b/command-snapshot.json
index 69009d712..7e29bd189 100644
--- a/command-snapshot.json
+++ b/command-snapshot.json
@@ -239,6 +239,7 @@
     "flagChars": ["c", "d", "m", "n", "p", "t"],
     "flags": [
       "api-version",
+      "excluded-metadata",
       "flags-dir",
       "from-org",
       "include-packages",
diff --git a/messages/manifest.generate.md b/messages/manifest.generate.md
index be2d55498..92285e5f1 100644
--- a/messages/manifest.generate.md
+++ b/messages/manifest.generate.md
@@ -19,6 +19,8 @@ Use --name to specify a custom name for the generated manifest if the pre-define
 
 To include multiple metadata components, either set multiple --metadata <name> flags or a single --metadata flag with multiple names separated by spaces. Enclose names that contain spaces in one set of double quotes. The same syntax applies to --include-packages and --source-dir.
 
+To build a manifest from the metadata in an org, use the --from-org flag. You can combine --from-org with the --metadata flag to include only certain metadata types, or with the --excluded-metadata flag to exclude certain metadata types. When building a manifest from an org, the command makes many concurrent API calls to discover the metadata that exists in the org. To limit the number of concurrent requests, use the SF_LIST_METADATA_BATCH_SIZE environment variable and set it to a size that works best for your org and environment. If you experience timeouts or inconsistent manifest contents, then setting this environment variable can improve accuracy. However, the command takes longer to run because it sends fewer requests at a time.
+
 # examples
 
 - Create a manifest for deploying or retrieving all Apex classes and custom objects:
@@ -37,10 +39,22 @@ To include multiple metadata components, either set multiple --metadata <name> f
 
   $ <%= config.bin %> <%= command.id %> --from-org test@myorg.com --include-packages unlocked
 
+- Create a manifest from specific metadata types in an org:
+
+  $ <%= config.bin %> <%= command.id %> --from-org test@myorg.com --metadata ApexClass,CustomObject,CustomLabels
+
+- Create a manifest from all metadata components in an org excluding specific metadata types:
+
+  $ <%= config.bin %> <%= command.id %> --from-org test@myorg.com --excluded-metadata StandardValueSet
+
 # flags.include-packages.summary
 
 Package types (managed, unlocked) whose metadata is included in the manifest; by default, metadata in managed and unlocked packages is excluded. Metadata in unmanaged packages is always included.
 
+# flags.excluded-metadata.summary
+
+Metadata types to exclude when building a manifest from an org. Specify the name of the type, not the name of a specific component.
+
 # flags.from-org.summary
 
 Username or alias of the org that contains the metadata components from which to build a manifest.
diff --git a/package.json b/package.json
index ae42abe06..71f4d296f 100644
--- a/package.json
+++ b/package.json
@@ -12,8 +12,8 @@
     "@salesforce/kit": "^3.2.3",
     "@salesforce/plugin-info": "^3.4.23",
     "@salesforce/sf-plugins-core": "^12.1.1",
-    "@salesforce/source-deploy-retrieve": "^12.10.3",
-    "@salesforce/source-tracking": "^7.3.4",
+    "@salesforce/source-deploy-retrieve": "^12.11.2",
+    "@salesforce/source-tracking": "^7.3.6",
     "@salesforce/ts-types": "^2.0.12",
     "ansis": "^3.4.0",
     "terminal-link": "^3.0.0"
diff --git a/src/commands/project/delete/source.ts b/src/commands/project/delete/source.ts
index 103cc03d3..67dc82847 100644
--- a/src/commands/project/delete/source.ts
+++ b/src/commands/project/delete/source.ts
@@ -404,9 +404,7 @@ export class Source extends SfCommand<DeleteSourceJson> {
         .filter(sourceComponentIsNotInMixedDeployDelete(this.mixedDeployDelete))
         .flatMap((c) =>
           // for custom labels, print each custom label to be deleted, not the whole file
-          isNonDecomposedCustomLabelsOrCustomLabel(c)
-            ? [`${c.type.name}:${c.fullName}`]
-            : [c.xml, ...c.walkContent()] ?? []
+          isNonDecomposedCustomLabelsOrCustomLabel(c) ? [`${c.type.name}:${c.fullName}`] : [c.xml, ...c.walkContent()]
         )
         .concat(this.mixedDeployDelete.delete.map((fr) => `${fr.fullName} (${fr.filePath})`));
 
diff --git a/src/commands/project/generate/manifest.ts b/src/commands/project/generate/manifest.ts
index 3d04f9d37..b800f4300 100644
--- a/src/commands/project/generate/manifest.ts
+++ b/src/commands/project/generate/manifest.ts
@@ -38,7 +38,7 @@ export type ManifestGenerateCommandResult = {
   path: string;
 };
 
-const xorFlags = ['metadata', 'source-dir', 'from-org'];
+const atLeastOneOfFlags = ['metadata', 'source-dir', 'from-org'];
 
 export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
   public static readonly summary = messages.getMessage('summary');
@@ -53,14 +53,14 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
     metadata: arrayWithDeprecation({
       char: 'm',
       summary: messages.getMessage('flags.metadata.summary'),
-      exactlyOne: xorFlags,
+      exclusive: ['source-dir'],
     }),
     'source-dir': arrayWithDeprecation({
       char: 'p',
       aliases: ['sourcepath'],
       deprecateAliases: true,
       summary: messages.getMessage('flags.source-dir.summary'),
-      exactlyOne: xorFlags,
+      exclusive: ['metadata'],
     }),
     name: Flags.string({
       char: 'n',
@@ -85,11 +85,18 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
       char: 'c',
       dependsOn: ['from-org'],
     }),
+    'excluded-metadata': Flags.string({
+      multiple: true,
+      delimiter: ',',
+      summary: messages.getMessage('flags.excluded-metadata.summary'),
+      dependsOn: ['from-org'],
+      exclusive: ['metadata'],
+    }),
     'from-org': Flags.custom({
       summary: messages.getMessage('flags.from-org.summary'),
-      exactlyOne: xorFlags,
       aliases: ['fromorg'],
       deprecateAliases: true,
+      exclusive: ['source-dir'],
       parse: async (input: string | undefined) => (input ? Org.create({ aliasOrUsername: input }) : undefined),
     })(),
     'output-dir': Flags.string({
@@ -102,6 +109,12 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
 
   public async run(): Promise<ManifestGenerateCommandResult> {
     const { flags } = await this.parse(ManifestGenerate);
+
+    // We need at least one of these flags (but could be more than 1): 'metadata', 'source-dir', 'from-org'
+    if (!Object.keys(flags).some((f) => atLeastOneOfFlags.includes(f))) {
+      throw Error(`provided flags must include at least one of: ${atLeastOneOfFlags.toString()}`);
+    }
+
     // convert the manifesttype into one of the "official" manifest names
     // if no manifesttype flag passed, use the manifestname?flag
     // if no manifestname flag, default to 'package.xml'
@@ -114,12 +127,14 @@ export class ManifestGenerate extends SfCommand<ManifestGenerateCommandResult> {
     const componentSet = await ComponentSetBuilder.build({
       apiversion: flags['api-version'] ?? (await getSourceApiVersion()),
       sourcepath: flags['source-dir'],
-      metadata: flags.metadata
-        ? {
-            metadataEntries: flags.metadata,
-            directoryPaths: await getPackageDirs(),
-          }
-        : undefined,
+      metadata:
+        flags.metadata ?? flags['excluded-metadata']
+          ? {
+              metadataEntries: flags.metadata ?? [],
+              directoryPaths: await getPackageDirs(),
+              excludedEntries: flags['excluded-metadata'],
+            }
+          : undefined,
       org: flags['from-org']
         ? {
             username: flags['from-org'].getUsername() as string,
diff --git a/test/nuts/manifest/manifestCreate.nut.ts b/test/nuts/manifest/manifestCreate.nut.ts
index ee9bd53e2..930703ff6 100644
--- a/test/nuts/manifest/manifestCreate.nut.ts
+++ b/test/nuts/manifest/manifestCreate.nut.ts
@@ -40,7 +40,7 @@ describe('project generate manifest', () => {
   });
 
   it('should produce a manifest (package.xml) for ApexClass', () => {
-    const result = execCmd<Dictionary>('force:source:manifest:create --metadata ApexClass --json', {
+    const result = execCmd<Dictionary>('project generate manifest --metadata ApexClass --json', {
       ensureExitCode: 0,
     }).jsonOutput?.result;
     expect(result).to.be.ok;
@@ -70,7 +70,7 @@ describe('project generate manifest', () => {
     const output = join('abc', 'def');
     const outputFile = join(output, 'destructiveChanges.xml');
     const result = execCmd<Dictionary>(
-      `force:source:manifest:create --metadata ApexClass --manifesttype destroy --outputdir ${output} --apiversion=51.0 --json`,
+      `project generate manifest --metadata ApexClass --manifesttype destroy --outputdir ${output} --apiversion=51.0 --json`,
       {
         ensureExitCode: 0,
       }
@@ -85,7 +85,7 @@ describe('project generate manifest', () => {
     const output = join('abc', 'def');
     const outputFile = join(output, 'myNewManifest.xml');
     const result = execCmd<Dictionary>(
-      `force:source:manifest:create --metadata ApexClass --manifestname myNewManifest --outputdir ${output} --json`,
+      `project generate manifest --metadata ApexClass --manifestname myNewManifest --outputdir ${output} --json`,
       {
         ensureExitCode: 0,
       }
@@ -96,50 +96,112 @@ describe('project generate manifest', () => {
 
   it('should produce a manifest in a directory with stdout output', () => {
     const output = join('abc', 'def');
-    const result = execCmd<Dictionary>(`force:source:manifest:create --metadata ApexClass --outputdir ${output}`, {
+    const result = execCmd<Dictionary>(`project generate manifest --metadata ApexClass --outputdir ${output}`, {
       ensureExitCode: 0,
     }).shellOutput;
     expect(result).to.include(`successfully wrote package.xml to ${output}`);
   });
 
   it('should produce a manifest with stdout output', () => {
-    const result = execCmd<Dictionary>('force:source:manifest:create --metadata ApexClass', {
+    const result = execCmd<Dictionary>('project generate manifest --metadata ApexClass', {
       ensureExitCode: 0,
     }).shellOutput;
     expect(result).to.include('successfully wrote package.xml');
   });
 
-  it('should produce a manifest from metadata in an org', async () => {
-    const manifestName = 'org-metadata.xml';
-    const result = execCmd<Dictionary>(`force:source:manifest:create --fromorg ${orgAlias} -n ${manifestName} --json`, {
-      ensureExitCode: 0,
-    }).jsonOutput?.result;
-    expect(result).to.be.ok;
-    expect(result).to.include({ path: manifestName, name: manifestName });
-    const stats = fs.statSync(join(session.project.dir, manifestName));
-    expect(stats.isFile()).to.be.true;
-    expect(stats.size).to.be.greaterThan(100);
-  });
-
-  it('should produce the same manifest from an org every time', async () => {
-    config.truncateThreshold = 0;
+  describe('from org', () => {
+    before(async () => {
+      // Deploy all source in the project to the org so there's some metadata in it.
+      execCmd<Dictionary>('project deploy start', { ensureExitCode: 0 });
+    });
 
-    execCmd<Dictionary>(`project generate manifest --from-org ${orgAlias} -n org-metadata-1.xml`, {
-      ensureExitCode: 0,
+    it('should produce a manifest from metadata in an org', async () => {
+      const manifestName = 'org-metadata.xml';
+      const result = execCmd<Dictionary>(`project generate manifest --fromorg ${orgAlias} -n ${manifestName} --json`, {
+        ensureExitCode: 0,
+      }).jsonOutput?.result;
+      expect(result).to.be.ok;
+      expect(result).to.include({ path: manifestName, name: manifestName });
+      const stats = fs.statSync(join(session.project.dir, manifestName));
+      expect(stats.isFile()).to.be.true;
+      expect(stats.size).to.be.greaterThan(100);
     });
-    const manifest1 = fs.readFileSync(join(session.project.dir, 'org-metadata-1.xml'), 'utf-8');
 
-    execCmd<Dictionary>(`project generate manifest --from-org ${orgAlias} -n org-metadata-2.xml`, {
-      ensureExitCode: 0,
+    it('should produce a manifest from an include list of metadata in an org', async () => {
+      const manifestName = 'org-metadata.xml';
+      const includeList = 'ApexClass:FileUtil*,PermissionSet,Flow';
+      execCmd<Dictionary>(
+        `project generate manifest --fromorg ${orgAlias} -n ${manifestName} --metadata ${includeList} --json`,
+        {
+          ensureExitCode: 0,
+        }
+      );
+      const manifestContents = fs.readFileSync(join(session.project.dir, manifestName), 'utf-8');
+
+      const expectedManifestContents =
+        '<?xml version="1.0" encoding="UTF-8"?>\n' +
+        '<Package xmlns="http://soap.sforce.com/2006/04/metadata">\n' +
+        '    <types>\n' +
+        '        <members>FileUtilities</members>\n' +
+        '        <members>FileUtilitiesTest</members>\n' +
+        '        <name>ApexClass</name>\n' +
+        '    </types>\n' +
+        '    <types>\n' +
+        '        <members>Create_property</members>\n' +
+        '        <name>Flow</name>\n' +
+        '    </types>\n' +
+        '    <types>\n' +
+        '        <members>dreamhouse</members>\n' +
+        '        <members>sfdcInternalInt__sfdc_scrt2</members>\n' +
+        '        <name>PermissionSet</name>\n' +
+        '    </types>\n' +
+        '    <version>61.0</version>\n' +
+        '</Package>\n';
+      expect(manifestContents).to.equal(expectedManifestContents);
     });
-    const manifest2 = fs.readFileSync(join(session.project.dir, 'org-metadata-2.xml'), 'utf-8');
 
-    execCmd<Dictionary>(`project generate manifest --from-org ${orgAlias} -n org-metadata-3.xml`, {
-      ensureExitCode: 0,
+    it('should produce a manifest from an excluded list of metadata in an org', async () => {
+      const manifestName = 'org-metadata.xml';
+      const excludedList = 'ApexClass,CustomObject,StandardValueSet';
+      execCmd<Dictionary>(
+        `project generate manifest --fromorg ${orgAlias} -n ${manifestName} --excluded-metadata ${excludedList} --json`,
+        {
+          ensureExitCode: 0,
+        }
+      );
+      const manifestContents = fs.readFileSync(join(session.project.dir, manifestName), 'utf-8');
+
+      // should NOT have these entries
+      expect(manifestContents).to.not.contain('<name>ApexClass</name>');
+      expect(manifestContents).to.not.contain('<name>CustomObject</name>');
+      expect(manifestContents).to.not.contain('<name>StandardValueSet</name>');
+
+      // should have these entries
+      expect(manifestContents).to.contain('<name>Layout</name>');
+      expect(manifestContents).to.contain('<name>CustomLabels</name>');
+      expect(manifestContents).to.contain('<name>Profile</name>');
     });
-    const manifest3 = fs.readFileSync(join(session.project.dir, 'org-metadata-3.xml'), 'utf-8');
 
-    expect(manifest1).to.equal(manifest2);
-    expect(manifest2).to.equal(manifest3);
+    it('should produce the same manifest from an org every time', async () => {
+      config.truncateThreshold = 0;
+
+      execCmd<Dictionary>(`project generate manifest --from-org ${orgAlias} -n org-metadata-1.xml`, {
+        ensureExitCode: 0,
+      });
+      const manifest1 = fs.readFileSync(join(session.project.dir, 'org-metadata-1.xml'), 'utf-8');
+
+      execCmd<Dictionary>(`project generate manifest --from-org ${orgAlias} -n org-metadata-2.xml`, {
+        ensureExitCode: 0,
+      });
+      const manifest2 = fs.readFileSync(join(session.project.dir, 'org-metadata-2.xml'), 'utf-8');
+
+      execCmd<Dictionary>(`project generate manifest --from-org ${orgAlias} -n org-metadata-3.xml`, {
+        ensureExitCode: 0,
+      });
+      const manifest3 = fs.readFileSync(join(session.project.dir, 'org-metadata-3.xml'), 'utf-8');
+
+      expect(manifest1).to.equal(manifest2);
+      expect(manifest2).to.equal(manifest3);
+    });
   });
 });
diff --git a/yarn.lock b/yarn.lock
index ca6da7810..687a9698f 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -1690,6 +1690,25 @@
     minimatch "^9.0.5"
     proxy-agent "^6.4.0"
 
+"@salesforce/source-deploy-retrieve@^12.11.2":
+  version "12.11.2"
+  resolved "https://registry.yarnpkg.com/@salesforce/source-deploy-retrieve/-/source-deploy-retrieve-12.11.2.tgz#8e789d88ce92ae024ea9cb57da88345b2d06b564"
+  integrity sha512-bfx0FnAJ9hfMB2ex9Jv1kfaKYuCe7Xe921ctVEOzIgwM9bisKYfL1NUKCiGwWYgS+dePcwmDcpJFJMr0CUu0ZA==
+  dependencies:
+    "@salesforce/core" "^8.8.0"
+    "@salesforce/kit" "^3.2.2"
+    "@salesforce/ts-types" "^2.0.12"
+    fast-levenshtein "^3.0.0"
+    fast-xml-parser "^4.5.1"
+    got "^11.8.6"
+    graceful-fs "^4.2.11"
+    ignore "^5.3.2"
+    isbinaryfile "^5.0.2"
+    jszip "^3.10.1"
+    mime "2.6.0"
+    minimatch "^9.0.5"
+    proxy-agent "^6.4.0"
+
 "@salesforce/source-testkit@^2.2.93":
   version "2.2.93"
   resolved "https://registry.yarnpkg.com/@salesforce/source-testkit/-/source-testkit-2.2.93.tgz#a4c537b328ab97a33f9411d5330f7d182f43ab50"
@@ -1706,15 +1725,15 @@
     shelljs "^0.8.4"
     sinon "^10.0.0"
 
-"@salesforce/source-tracking@^7.3.4":
-  version "7.3.4"
-  resolved "https://registry.yarnpkg.com/@salesforce/source-tracking/-/source-tracking-7.3.4.tgz#6e51ffb0c6305086c142f86ed17432cfb37298ba"
-  integrity sha512-Qs2GWPaF8GrIvEZyVqX9zmk80BZAzKxirbnfGk+eB0Nig3/Yh01PLdjH5ctRxZpAvraXYZqConIyUxztwT16pA==
+"@salesforce/source-tracking@^7.3.6":
+  version "7.3.6"
+  resolved "https://registry.yarnpkg.com/@salesforce/source-tracking/-/source-tracking-7.3.6.tgz#70d1ffbe511394f64b5a28e0e5af88b8aed45c96"
+  integrity sha512-U++xMp9gdU+Iq8C9vYOVpzMSkB2lcYMCs7VpC7h518pt1KC/GRV0ufWI6qwcSxZzsZMrPCpCdhGITpAgmM5YnA==
   dependencies:
     "@oclif/core" "^4.2.0"
     "@salesforce/core" "^8.8.0"
     "@salesforce/kit" "^3.2.3"
-    "@salesforce/source-deploy-retrieve" "^12.10.3"
+    "@salesforce/source-deploy-retrieve" "^12.11.2"
     "@salesforce/ts-types" "^2.0.12"
     fast-xml-parser "^4.5.1"
     graceful-fs "^4.2.11"