diff --git a/src/lib/plugins/get-deps-from-plugin.ts b/src/lib/plugins/get-deps-from-plugin.ts
index 57240107f6e..79e91696e06 100644
--- a/src/lib/plugins/get-deps-from-plugin.ts
+++ b/src/lib/plugins/get-deps-from-plugin.ts
@@ -1,4 +1,6 @@
 import * as debugModule from 'debug';
+import * as pathLib from 'path';
+import chalk from 'chalk';
 import { legacyPlugin as pluginApi } from '@snyk/cli-interface';
 import { find } from '../find-files';
 import { Options, TestOptions, MonitorOptions } from '../types';
@@ -17,6 +19,7 @@ import analytics = require('../analytics');
 import { convertSingleResultToMultiCustom } from './convert-single-splugin-res-to-multi-custom';
 import { convertMultiResultToMultiCustom } from './convert-multi-plugin-res-to-multi-custom';
 import { processYarnWorkspaces } from './nodejs-plugin/yarn-workspaces-parser';
+import { ScannedProject } from '@snyk/cli-interface/legacy/common';
 
 const debug = debugModule('snyk-test');
 
@@ -42,7 +45,7 @@ export async function getDepsFromPlugin(
     const scanType = options.yarnWorkspaces ? 'yarnWorkspaces' : 'allProjects';
     const levelsDeep = options.detectionDepth;
     const ignore = options.exclude ? options.exclude.split(',') : [];
-    const { files: targetFiles } = await find(
+    const { files: targetFiles, allFilesFound } = await find(
       root,
       ignore,
       multiProjectProcessors[scanType].files,
@@ -62,8 +65,9 @@ export async function getDepsFromPlugin(
       options,
       targetFiles,
     );
+    const scannedProjects = inspectRes.scannedProjects;
     const analyticData = {
-      scannedProjects: inspectRes.scannedProjects.length,
+      scannedProjects: scannedProjects.length,
       targetFiles,
       packageManagers: targetFiles.map((file) =>
         detectPackageManagerFromFile(file),
@@ -72,6 +76,18 @@ export async function getDepsFromPlugin(
       ignore,
     };
     analytics.add(scanType, analyticData);
+    debug(
+      `Found ${scannedProjects.length} projects from ${allFilesFound.length} detected manifests`,
+    );
+    const userWarningMessage = warnSomeGradleManifestsNotScanned(
+      scannedProjects,
+      allFilesFound,
+      root,
+    );
+
+    if (!options.json && userWarningMessage) {
+      console.warn(chalk.bold.red(userWarningMessage));
+    }
     return inspectRes;
   }
 
@@ -105,3 +121,35 @@ export async function getDepsFromPlugin(
   );
   return convertMultiResultToMultiCustom(inspectRes, options.packageManager);
 }
+
+export function warnSomeGradleManifestsNotScanned(
+  scannedProjects: ScannedProject[],
+  allFilesFound: string[],
+  root: string,
+): string | null {
+  const gradleTargetFilesFilter = (targetFile) =>
+    targetFile &&
+    (targetFile.endsWith('build.gradle') ||
+      targetFile.endsWith('build.gradle.kts'));
+  const scannedGradleFiles = scannedProjects
+    .map((p) => {
+      const targetFile = p.meta?.targetFile || p.targetFile;
+      return targetFile ? pathLib.resolve(root, targetFile) : null;
+    })
+    .filter(gradleTargetFilesFilter);
+  const detectedGradleFiles = allFilesFound.filter(gradleTargetFilesFilter);
+  const diff = detectedGradleFiles.filter(
+    (file) => !scannedGradleFiles.includes(file),
+  );
+
+  debug(
+    `These Gradle manifests did not return any dependency results:\n${diff.join(
+      ',\n',
+    )}`,
+  );
+
+  if (diff.length > 0) {
+    return `✗ ${diff.length}/${detectedGradleFiles.length} detected Gradle manifests did not return dependencies.\nThey may have errored or were not included as part of a multi-project build. You may need to scan them individually with --file=path/to/file. Run with \`-d\` for more info.`;
+  }
+  return null;
+}
diff --git a/test/acceptance/cli-test/cli-test.all-projects.spec.ts b/test/acceptance/cli-test/cli-test.all-projects.spec.ts
index 90862be8034..2e9a07a69f0 100644
--- a/test/acceptance/cli-test/cli-test.all-projects.spec.ts
+++ b/test/acceptance/cli-test/cli-test.all-projects.spec.ts
@@ -4,40 +4,112 @@ import * as depGraphLib from '@snyk/dep-graph';
 import { CommandResult } from '../../../src/cli/commands/types';
 import { AcceptanceTests } from './cli-test.acceptance.test';
 import { getWorkspaceJSON } from '../workspace-helper';
+import * as getDepsFromPlugin from '../../../src/lib/plugins/get-deps-from-plugin';
+
+const simpleGradleGraph = depGraphLib.createFromJSON({
+  schemaVersion: '1.2.0',
+  pkgManager: {
+    name: 'gradle',
+  },
+  pkgs: [
+    {
+      id: 'gradle-monorepo@0.0.0',
+      info: {
+        name: 'gradle-monorepo',
+        version: '0.0.0',
+      },
+    },
+  ],
+  graph: {
+    rootNodeId: 'root-node',
+    nodes: [
+      {
+        nodeId: 'root-node',
+        pkgId: 'gradle-monorepo@0.0.0',
+        deps: [],
+      },
+    ],
+  },
+});
 
 export const AllProjectsTests: AcceptanceTests = {
   language: 'Mixed',
   tests: {
-    '`test kotlin-monorepo --all-projects` scans kotlin files': (
+    '`test gradle-with-orphaned-build-file --all-projects` warns user': (
       params,
       utils,
     ) => async (t) => {
       utils.chdirWorkspaces();
-      const simpleGradleGraph = depGraphLib.createFromJSON({
-        schemaVersion: '1.2.0',
-        pkgManager: {
-          name: 'gradle',
-        },
-        pkgs: [
-          {
-            id: 'gradle-monorepo@0.0.0',
-            info: {
-              name: 'gradle-monorepo',
-              version: '0.0.0',
-            },
-          },
-        ],
-        graph: {
-          rootNodeId: 'root-node',
-          nodes: [
-            {
-              nodeId: 'root-node',
-              pkgId: 'gradle-monorepo@0.0.0',
-              deps: [],
+      const plugin = {
+        async inspect() {
+          return {
+            plugin: {
+              name: 'bundled:gradle',
+              runtime: 'unknown',
+              meta: {},
             },
-          ],
+            scannedProjects: [
+              {
+                meta: {
+                  gradleProjectName: 'root-proj',
+                  versionBuildInfo: {
+                    gradleVersion: '6.5',
+                  },
+                  targetFile: 'build.gradle',
+                },
+                depGraph: simpleGradleGraph,
+              },
+              {
+                meta: {
+                  gradleProjectName: 'root-proj/subproj',
+                  versionBuildInfo: {
+                    gradleVersion: '6.5',
+                  },
+                  targetFile: 'subproj/build.gradle',
+                },
+                depGraph: simpleGradleGraph,
+              },
+            ],
+          };
         },
-      });
+      };
+      const loadPlugin = sinon.stub(params.plugins, 'loadPlugin');
+      t.teardown(loadPlugin.restore);
+      loadPlugin.withArgs('gradle').returns(plugin);
+      loadPlugin.callThrough();
+      // read data from console.log
+      let stdoutMessages = '';
+      const stubConsoleLog = (msg: string) => (stdoutMessages += msg);
+      const stubbedConsole = sinon
+        .stub(console, 'warn')
+        .callsFake(stubConsoleLog);
+      const result: CommandResult = await params.cli.test(
+        'gradle-with-orphaned-build-file',
+        {
+          allProjects: true,
+          detectionDepth: 3,
+        },
+      );
+      t.same(
+        stdoutMessages,
+        '✗ 1/3 detected Gradle manifests did not return dependencies.\n' +
+          'They may have errored or were not included as part of a multi-project build. You may need to scan them individually with --file=path/to/file. Run with `-d` for more info.',
+      );
+      stubbedConsole.restore();
+      t.ok(stubbedConsole.calledOnce);
+      t.ok(loadPlugin.withArgs('gradle').calledOnce, 'calls gradle plugin');
+
+      t.match(
+        result.getDisplayResults(),
+        'Tested 2 projects',
+        'Detected 2 projects',
+      );
+    },
+    '`test kotlin-monorepo --all-projects` scans kotlin files': (
+      params,
+      utils,
+    ) => async (t) => {
+      utils.chdirWorkspaces();
       const plugin = {
         async inspect() {
           return {
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/build.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/build.gradle
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/orphaned/build.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/orphaned/build.gradle
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/settings.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/settings.gradle
new file mode 100644
index 00000000000..90289e8a32b
--- /dev/null
+++ b/test/acceptance/workspaces/gradle-with-orphaned-build-file/settings.gradle
@@ -0,0 +1,5 @@
+rootProject.name = 'root-proj'
+
+include 'subproj'
+
+
diff --git a/test/acceptance/workspaces/gradle-with-orphaned-build-file/subproj/build.gradle b/test/acceptance/workspaces/gradle-with-orphaned-build-file/subproj/build.gradle
new file mode 100644
index 00000000000..301e7be03bc
--- /dev/null
+++ b/test/acceptance/workspaces/gradle-with-orphaned-build-file/subproj/build.gradle
@@ -0,0 +1,51 @@
+apply plugin: 'java'
+apply plugin: 'maven'
+
+group = 'com.github.jitpack'
+
+sourceCompatibility = 1.8 // java 8
+targetCompatibility = 1.8
+
+repositories {
+  mavenCentral()
+}
+
+dependencies {
+  // Gradle 3+ will not pick up "compile" dependencies for "compileOnly"
+  // Gradle 2 will, so for configuration-matching tests we use "runtime"
+  runtime 'com.google.guava:guava:18.0'
+  runtime 'batik:batik-dom:1.6'
+  runtime 'commons-discovery:commons-discovery:0.2'
+  compileOnly 'axis:axis:1.3'
+  runtime 'com.android.tools.build:builder:2.3.0'
+}
+
+task sourcesJar(type: Jar, dependsOn: classes) {
+    classifier = 'sources'
+    from sourceSets.main.allSource
+}
+
+task javadocJar(type: Jar, dependsOn: javadoc) {
+    classifier = 'javadoc'
+    from javadoc.destinationDir
+}
+
+artifacts {
+    archives sourcesJar
+    archives javadocJar
+}
+
+// To specify a license in the pom:
+install {
+  repositories.mavenInstaller {
+    pom.project {
+      licenses {
+        license {
+          name 'The Apache Software License, Version 2.0'
+          url 'http://www.apache.org/licenses/LICENSE-2.0.txt'
+          distribution 'repo'
+        }
+      }
+    }
+  }
+}