diff --git a/CHANGELOG.md b/CHANGELOG.md
index daa85e021..d54ddd1ed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
+## [Unreleased]
+
+### Fixed
+- Socket facts for a Maven or Gradle build pointed elsewhere with `-f` or `-p` are now written into that build's own directory, where their paths resolve.
+
 ## [1.6.1](https://github.com/SocketDev/socket-cli/releases/tag/v1.6.1) - 2026-10-08
 
 ### Changed
diff --git a/src/commands/manifest/generate-recursive-manifests.mts b/src/commands/manifest/generate-recursive-manifests.mts
index fd329f20c..70f76047e 100644
--- a/src/commands/manifest/generate-recursive-manifests.mts
+++ b/src/commands/manifest/generate-recursive-manifests.mts
@@ -185,10 +185,13 @@ async function runEcosystemCandidates({
       }
 
       covered.add(dir)
+      // `-f`/`-p` can root the reactor away from `dir`.
+      // eslint-disable-next-line no-await-in-loop
+      const buildRoot = await realpathOrResolved(path.dirname(result.factsPath))
       // eslint-disable-next-line no-await-in-loop
       const resolvedSubprojectDirs = await Promise.all(
         result.projects.map(project =>
-          realpathOrResolved(path.resolve(dir, project.subprojectDir)),
+          realpathOrResolved(path.resolve(buildRoot, project.subprojectDir)),
         ),
       )
       for (const subprojectDir of resolvedSubprojectDirs) {
@@ -203,7 +206,10 @@ async function runEcosystemCandidates({
         // meaningful data point, not a redundant one. Never suppress its own
         // build-root invocation, regardless of which reactor(s) also
         // incorporate it or the order candidates happen to be discovered in.
-        if (subprojectDir.startsWith(`${dir}${path.sep}`)) {
+        if (
+          subprojectDir === buildRoot ||
+          subprojectDir.startsWith(`${buildRoot}${path.sep}`)
+        ) {
           covered.add(subprojectDir)
         }
       }
@@ -218,7 +224,7 @@ async function runEcosystemCandidates({
   return outcomes
 }
 
-// Generates one .socket.facts.json per independent gradle/sbt/maven build
+// Generates one Socket facts file per independent gradle/sbt/maven build
 // root under `cwd`. Coverage is tracked per ecosystem via the facts SBOM's
 // own projects[].subprojectDir, not by pruning the whole discovered subtree,
 // so an unrelated nested project a reactor doesn't declare still gets its
diff --git a/src/commands/manifest/generate-recursive-manifests.test.mts b/src/commands/manifest/generate-recursive-manifests.test.mts
index 041a223aa..fa90eb4cc 100644
--- a/src/commands/manifest/generate-recursive-manifests.test.mts
+++ b/src/commands/manifest/generate-recursive-manifests.test.mts
@@ -164,6 +164,59 @@ describe('generateRecursiveManifests', () => {
     },
   )
 
+  it('judges coverage against the reported build root, not the discovery directory', async () => {
+    const outer = await fs.realpath(
+      await fs.mkdtemp(path.join(tmpdir(), 'relocated-build-root-')),
+    )
+    const buildRoot = path.join(outer, 'build')
+    const member = path.join(buildRoot, 'member')
+    const escaped = path.join(outer, 'escaped')
+    try {
+      for (const dir of [outer, member, escaped]) {
+        // eslint-disable-next-line no-await-in-loop
+        await fs.mkdir(dir, { recursive: true })
+        // eslint-disable-next-line no-await-in-loop
+        await fs.writeFile(path.join(dir, 'pom.xml'), '<project/>')
+      }
+      vi.mocked(runManifestFacts).mockImplementation(async ({ cwd }) => {
+        if (cwd === outer) {
+          return {
+            factsPath: path.join(buildRoot, 'x.xml.socket.facts.json'),
+            projects: [
+              {
+                type: 'maven',
+                name: 'member',
+                subprojectDir: 'member',
+                dependencies: [],
+              },
+              {
+                type: 'maven',
+                name: 'escaped',
+                subprojectDir: '../escaped',
+                dependencies: [],
+              },
+            ],
+          }
+        }
+        return {
+          factsPath: path.join(cwd, 'pom.xml.socket.facts.json'),
+          projects: [],
+        }
+      })
+
+      const outcomes = await generateRecursiveManifests({
+        cwd: outer,
+        verbose: false,
+      })
+
+      const byDir = new Map(outcomes.map(o => [o.dir, o.status]))
+      expect(byDir.get(member)).toBe('skippedCovered')
+      expect(byDir.get(escaped)).toBe('generated')
+    } finally {
+      await fs.rm(outer, { recursive: true, force: true })
+    }
+  })
+
   it("runs both ecosystems unconditionally at a dual-marker directory (matches auto's existing behavior)", async () => {
     vi.mocked(runManifestFacts).mockImplementation(async ({ cwd }) => ({
       factsPath: path.join(cwd, '.socket.facts.json'),
diff --git a/src/commands/manifest/run-manifest-facts.mts b/src/commands/manifest/run-manifest-facts.mts
index cecf4f9d3..520bf68a4 100644
--- a/src/commands/manifest/run-manifest-facts.mts
+++ b/src/commands/manifest/run-manifest-facts.mts
@@ -79,8 +79,6 @@ export async function runManifestFacts({
   verbose: boolean
   withFiles?: boolean | undefined
 }): Promise<RunManifestFactsOutcome> {
-  const factsPath = path.join(cwd, constants.DOT_SOCKET_DOT_FACTS_JSON)
-
   let resolvedJavaHome: string | undefined
   if (javaHome) {
     const expanded = expandEnvVarRefs(javaHome)
@@ -160,7 +158,8 @@ export async function runManifestFacts({
     )
     return null
   }
-  const { artifactPaths, code, facts, report, stderr, stdout } = result
+  const { artifactPaths, buildRoot, code, facts, report, stderr, stdout } =
+    result
 
   const rendered = renderResolutionErrorReport(
     report.failures,
@@ -230,6 +229,17 @@ export async function runManifestFacts({
     return
   }
 
+  if (!buildRoot) {
+    process.exitCode = 1
+    logger.fail(
+      `The ${ecosystem} build did not report its root directory, so its Socket facts file cannot be placed.`,
+    )
+    return null
+  }
+  // Every path in the facts is relative to the build root, which `-f`/`-p`
+  // can move away from cwd.
+  const factsPath = path.join(buildRoot, constants.DOT_SOCKET_DOT_FACTS_JSON)
+
   const socketCliVersion = constants.ENV.INLINED_SOCKET_CLI_VERSION
   if (facts.metadata && socketCliVersion) {
     facts.metadata.socketCliVersion = socketCliVersion
diff --git a/src/commands/manifest/run-manifest-facts.test.mts b/src/commands/manifest/run-manifest-facts.test.mts
index 9c735cfc0..492e64d2a 100644
--- a/src/commands/manifest/run-manifest-facts.test.mts
+++ b/src/commands/manifest/run-manifest-facts.test.mts
@@ -17,8 +17,9 @@ import type { SidecarAccumulator } from './scripts/sidecar.mts'
 
 const ENV_VAR = 'SOCKET_TEST_JAVA_HOME'
 
-function okResult(): ManifestRunResult {
+function okResult(buildRoot: string): ManifestRunResult {
   return {
+    buildRoot,
     code: 0,
     facts: {
       components: [{ id: 'a', type: 'maven', name: 'a' }],
@@ -63,7 +64,7 @@ describe('runManifestFacts - javaHome', () => {
   })
 
   it('passes a literal javaHome straight through as JAVA_HOME', async () => {
-    vi.mocked(runManifestScript).mockResolvedValue(okResult())
+    vi.mocked(runManifestScript).mockResolvedValue(okResult(cwd))
     await runManifestFacts({ ...baseArgs, cwd, javaHome: '/opt/jdk-17' })
     const opts = vi.mocked(runManifestScript).mock.calls[0]?.[1]
     expect(opts?.env?.['JAVA_HOME']).toBe('/opt/jdk-17')
@@ -71,7 +72,7 @@ describe('runManifestFacts - javaHome', () => {
 
   it('expands $VAR and ${VAR} references against the CLI process env', async () => {
     process.env[ENV_VAR] = '/opt/jdk-11'
-    vi.mocked(runManifestScript).mockResolvedValue(okResult())
+    vi.mocked(runManifestScript).mockResolvedValue(okResult(cwd))
     await runManifestFacts({
       ...baseArgs,
       cwd,
@@ -82,7 +83,7 @@ describe('runManifestFacts - javaHome', () => {
   })
 
   it('fails closed without invoking the build tool when the referenced var is unset', async () => {
-    vi.mocked(runManifestScript).mockResolvedValue(okResult())
+    vi.mocked(runManifestScript).mockResolvedValue(okResult(cwd))
     const result = await runManifestFacts({
       ...baseArgs,
       cwd,
@@ -94,7 +95,7 @@ describe('runManifestFacts - javaHome', () => {
   })
 
   it('leaves the environment untouched when javaHome is unset', async () => {
-    vi.mocked(runManifestScript).mockResolvedValue(okResult())
+    vi.mocked(runManifestScript).mockResolvedValue(okResult(cwd))
     await runManifestFacts({ ...baseArgs, cwd })
     const opts = vi.mocked(runManifestScript).mock.calls[0]?.[1]
     expect(opts?.env).toBeUndefined()
@@ -115,7 +116,7 @@ describe('runManifestFacts - sidecar', () => {
   })
 
   it('keys the sidecar by the symlink-resolved factsPath, not the raw cwd-joined one', async () => {
-    const result = okResult()
+    const result = okResult(cwd)
     result.facts.projects = [
       {
         type: 'maven',
@@ -139,7 +140,7 @@ describe('runManifestFacts - sidecar', () => {
     expect(bucket?.projects.find(m => m.name === 'app')).toBeDefined()
   })
   it('stamps the inlined socket-cli version into the written facts metadata', async () => {
-    const result = okResult()
+    const result = okResult(cwd)
     result.facts.metadata = {
       format: 'socket-facts-sbom',
       tool: 'maven',
@@ -160,6 +161,44 @@ describe('runManifestFacts - sidecar', () => {
   })
 })
 
+describe('runManifestFacts - build root', () => {
+  let cwd = ''
+
+  beforeEach(async () => {
+    cwd = await fs.mkdtemp(path.join(tmpdir(), 'run-manifest-facts-'))
+    vi.mocked(runManifestScript).mockReset()
+    process.exitCode = undefined
+  })
+  afterEach(async () => {
+    await fs.rm(cwd, { recursive: true, force: true })
+    process.exitCode = undefined
+  })
+
+  it('writes the facts file into the build root the tool reports', async () => {
+    const buildRoot = path.join(cwd, 'sub')
+    await fs.mkdir(buildRoot)
+    vi.mocked(runManifestScript).mockResolvedValue(okResult(buildRoot))
+
+    const outcome = await runManifestFacts({ ...baseArgs, cwd })
+
+    expect(outcome?.factsPath).toBe(path.join(buildRoot, '.socket.facts.json'))
+    expect(await fs.readdir(buildRoot)).toEqual(['.socket.facts.json'])
+  })
+
+  it('fails without writing when the build did not report its root', async () => {
+    vi.mocked(runManifestScript).mockResolvedValue({
+      ...okResult(cwd),
+      buildRoot: undefined,
+    })
+
+    const outcome = await runManifestFacts({ ...baseArgs, cwd })
+
+    expect(outcome).toBeNull()
+    expect(process.exitCode).toBe(1)
+    expect(await fs.readdir(cwd)).toEqual([])
+  })
+})
+
 describe('runManifestFacts - sbt build detection', () => {
   let cwd = ''
 
@@ -196,7 +235,7 @@ describe('runManifestFacts - sbt build detection', () => {
       } else {
         await fs.writeFile(path.join(cwd, marker), '')
       }
-      vi.mocked(runManifestScript).mockResolvedValue(okResult())
+      vi.mocked(runManifestScript).mockResolvedValue(okResult(cwd))
 
       await runManifestFacts({ ...baseArgs, cwd, ecosystem: 'sbt' })
 
diff --git a/src/commands/manifest/scripts/assemble.test.mts b/src/commands/manifest/scripts/assemble.test.mts
index 40fc827e7..284cba72e 100644
--- a/src/commands/manifest/scripts/assemble.test.mts
+++ b/src/commands/manifest/scripts/assemble.test.mts
@@ -187,3 +187,13 @@ describe('records → assemble → sidecar', () => {
     })
   })
 })
+
+describe('parseRecords', () => {
+  it('reads the build root the build reports', () => {
+    expect(
+      parseRecords(
+        ['meta\tmaven\t3.9.6\t17', 'buildRoot\t/repo/sub'].join('\n'),
+      ).buildRoot,
+    ).toBe('/repo/sub')
+  })
+})
diff --git a/src/commands/manifest/scripts/maven-extension/src/main/java/tech/coana/socket/SocketFactsRecordsEngine.java b/src/commands/manifest/scripts/maven-extension/src/main/java/tech/coana/socket/SocketFactsRecordsEngine.java
index f5074848b..8facd1502 100644
--- a/src/commands/manifest/scripts/maven-extension/src/main/java/tech/coana/socket/SocketFactsRecordsEngine.java
+++ b/src/commands/manifest/scripts/maven-extension/src/main/java/tech/coana/socket/SocketFactsRecordsEngine.java
@@ -93,6 +93,7 @@ public void run(MavenSession session, List<MavenProject> reactor, File rootDir,
 
     List<String> lines = new ArrayList<>();
     rec(lines, "meta", "maven", mavenVersion, System.getProperty("java.version"));
+    rec(lines, "buildRoot", rootDir.getAbsolutePath());
 
     for (MavenProject module : reactor) {
       // No basedir: Maven's stand-in project for a directory without a POM. Skipping it lets Maven's
diff --git a/src/commands/manifest/scripts/records.mts b/src/commands/manifest/scripts/records.mts
index 14a776e84..a5207d907 100644
--- a/src/commands/manifest/scripts/records.mts
+++ b/src/commands/manifest/scripts/records.mts
@@ -10,6 +10,7 @@ import type {
 //   <tag>\t<field>\t<field>...
 //
 //   meta        tool  toolVersion  javaVersion
+//   buildRoot   path                                     (absolute; the facts file's directory)
 //   project     projectKey  group  name  version  dir
 //   projectSrc  projectKey  path                         (--with-files only)
 //   projectTgt  projectKey  path                         (--with-files only)
@@ -67,6 +68,8 @@ export type ParsedRecords = {
   tool: string
   toolVersion: string
   javaVersion: string
+  // Absolute directory the build is rooted at; the facts file is written there.
+  buildRoot: string
   projects: Map<string, RawProject>
   roots: Map<string, RawRoot>
   scannedConfigs: string[]
@@ -100,6 +103,7 @@ export function parseRecords(text: string): ParsedRecords {
     tool: '',
     toolVersion: '',
     javaVersion: '',
+    buildRoot: '',
     projects: new Map(),
     roots: new Map(),
     scannedConfigs: [],
@@ -152,6 +156,9 @@ export function parseRecords(text: string): ParsedRecords {
         result.toolVersion = f[2] ?? ''
         result.javaVersion = f[3] ?? ''
         break
+      case 'buildRoot':
+        result.buildRoot = f[1] ?? ''
+        break
       case 'project': {
         const p = project(f[1] ?? '')
         p.group = f[2] ?? ''
diff --git a/src/commands/manifest/scripts/run.mts b/src/commands/manifest/scripts/run.mts
index fda242661..993945e0c 100644
--- a/src/commands/manifest/scripts/run.mts
+++ b/src/commands/manifest/scripts/run.mts
@@ -49,6 +49,8 @@ export type ManifestScriptOptions = {
 export type ManifestRunResult = {
   code: number
   facts: SocketFactsSbom
+  // Undefined when the build did not report it.
+  buildRoot: string | undefined
   report: ResolutionReport
   artifactPaths: ResolvedArtifactPaths
   // Captured build-tool output (empty when stdio is 'inherit').
@@ -139,8 +141,10 @@ async function assembleFromRecords(
   const text = existsSync(recordsFile)
     ? await fs.readFile(recordsFile, 'utf8')
     : ''
-  const { artifactPaths, facts, report } = assembleFacts(parseRecords(text))
+  const parsed = parseRecords(text)
+  const { artifactPaths, facts, report } = assembleFacts(parsed)
   return {
+    buildRoot: parsed.buildRoot || undefined,
     code: out.code,
     facts,
     report,
diff --git a/src/commands/manifest/scripts/socket-facts.init.gradle b/src/commands/manifest/scripts/socket-facts.init.gradle
index 184fcfece..299f1fd56 100644
--- a/src/commands/manifest/scripts/socket-facts.init.gradle
+++ b/src/commands/manifest/scripts/socket-facts.init.gradle
@@ -473,6 +473,7 @@ rootProject { rp ->
   // task actions. The Socket CLI disables the cache for this run, but hoisting is cheap insurance.
   def recordsFileOverride = gradle.socketProp.call(rp, 'socket.recordsFile')?.toString()
   def defaultRecordsFile = new File(rp.projectDir, '.socket.facts.records.tsv').absolutePath
+  def buildRootPath = rp.projectDir.absolutePath
   // `sources`/`targets` are --with-files-only; a plain run emits only the graph fields.
   def withFilesProjects = gradle.socketProp.call(rp, 'socket.withFiles')?.toString()?.toLowerCase() == 'true'
 
@@ -493,6 +494,7 @@ rootProject { rp ->
       def rec = { List fields -> lines << fields.collect { esc(it) }.join('\t') }
 
       rec(['meta', 'gradle', gradle.gradleVersion, System.getProperty('java.version')])
+      rec(['buildRoot', buildRootPath])
 
       // One `project` record per build module (sources/targets only with --with-files).
       def projectsInfo
diff --git a/src/commands/manifest/scripts/socket-facts.plugin.scala b/src/commands/manifest/scripts/socket-facts.plugin.scala
index e14edfe3a..993aa8ddd 100644
--- a/src/commands/manifest/scripts/socket-facts.plugin.scala
+++ b/src/commands/manifest/scripts/socket-facts.plugin.scala
@@ -98,6 +98,7 @@ object SocketFactsPlugin extends AutoPlugin {
       }
 
       rec("meta", "sbt", extracted.getOpt(sbtVersion).getOrElse(""), sys.props.getOrElse("java.version", ""))
+      rec("buildRoot", rootCanonPath.toString)
 
       // One `project` record per build module (sources/targets only with --with-files). Excluded
       // subprojects are omitted (they were also skipped during resolution above).