diff --git a/packages/gatsby/src/internal-plugins/query-runner/__tests__/query-compiler.js b/packages/gatsby/src/internal-plugins/query-runner/__tests__/query-compiler.js
new file mode 100644
index 0000000000000..6da385f8dde73
--- /dev/null
+++ b/packages/gatsby/src/internal-plugins/query-runner/__tests__/query-compiler.js
@@ -0,0 +1,100 @@
+jest.mock(`glob`, () => {
+  const sync = jest.fn().mockImplementation(() => [])
+  return {
+    sync,
+  }
+})
+const path = require(`path`)
+const glob = require(`glob`)
+const { resolveThemes, Runner } = require(`../query-compiler`)
+
+const base = path.resolve(``)
+
+describe(`Runner`, () => {
+  beforeEach(() => {
+    glob.sync.mockClear()
+  })
+
+  it(`returns a file parser instance`, async () => {
+    const runner = new Runner(base, [], {})
+
+    const parser = await runner.parseEverything()
+
+    expect(parser).toEqual(new Map())
+  })
+
+  describe(`expected directories`, () => {
+    it(`compiles src directory`, async () => {
+      const runner = new Runner(base, [], {})
+
+      await runner.parseEverything()
+
+      expect(glob.sync).toHaveBeenCalledWith(
+        expect.stringContaining(path.join(base, `src`)),
+        expect.any(Object)
+      )
+    })
+
+    it(`compiles fragments directory`, async () => {
+      const runner = new Runner(base, [], {})
+
+      await runner.parseEverything()
+
+      expect(glob.sync).toHaveBeenCalledWith(
+        expect.stringContaining(path.join(base, `src`)),
+        expect.any(Object)
+      )
+    })
+
+    it(`compiles themes directory(s)`, async () => {
+      const theme = `gatsby-theme-whatever`
+      const runner = new Runner(
+        base,
+        [path.join(base, `node_modules`, theme)],
+        {}
+      )
+
+      await runner.parseEverything()
+
+      expect(glob.sync).toHaveBeenCalledWith(
+        expect.stringContaining(path.join(base, `node_modules`, theme)),
+        expect.any(Object)
+      )
+    })
+  })
+})
+
+describe(`resolveThemes`, () => {
+  it(`returns empty array if zero themes detected`, () => {
+    ;[
+      [],
+      [{ resolve: path.join(base, `gatsby-plugin-whatever`) }],
+      undefined,
+    ].forEach(testRun => {
+      expect(resolveThemes(testRun)).toEqual([])
+    })
+  })
+
+  it(`returns plugins matching gatsby-theme prefix`, () => {
+    const theme = `gatsby-theme-example`
+    expect(
+      resolveThemes([
+        {
+          resolve: path.join(base, `gatsby-theme-example`),
+        },
+      ])
+    ).toEqual([expect.stringContaining(theme)])
+  })
+
+  it(`handles scoped packages`, () => {
+    const theme = `@dschau/gatsby-theme-example`
+
+    expect(
+      resolveThemes([
+        {
+          resolve: path.join(base, theme),
+        },
+      ])
+    ).toEqual([expect.stringContaining(theme.split(`/`).join(path.sep))])
+  })
+})
diff --git a/packages/gatsby/src/internal-plugins/query-runner/query-compiler.js b/packages/gatsby/src/internal-plugins/query-runner/query-compiler.js
index e37e85e3829ab..002a888a50419 100644
--- a/packages/gatsby/src/internal-plugins/query-runner/query-compiler.js
+++ b/packages/gatsby/src/internal-plugins/query-runner/query-compiler.js
@@ -64,15 +64,24 @@ const validationRules = [
 let lastRunHadErrors = null
 const overlayErrorID = `graphql-compiler`
 
+const resolveThemes = (plugins = []) =>
+  plugins.reduce((merged, plugin) => {
+    if (plugin.resolve.includes(`gatsby-theme-`)) {
+      merged.push(plugin.resolve)
+    }
+    return merged
+  }, [])
+
 class Runner {
-  baseDir: string
+  base: string
+  additional: string[]
   schema: GraphQLSchema
   errors: string[]
   fragmentsDir: string
 
-  constructor(baseDir: string, fragmentsDir: string, schema: GraphQLSchema) {
-    this.baseDir = baseDir
-    this.fragmentsDir = fragmentsDir
+  constructor(base: string, additional: string[], schema: GraphQLSchema) {
+    this.base = base
+    this.additional = additional
     this.schema = schema
   }
 
@@ -91,14 +100,21 @@ class Runner {
   }
 
   async parseEverything() {
-    // FIXME: this should all use gatsby's configuration to determine parsable
-    // files (and how to parse them)
-    let files = glob.sync(`${this.fragmentsDir}/**/*.+(t|j)s?(x)`, {
-      nodir: true,
-    })
-    files = files.concat(
-      glob.sync(`${this.baseDir}/**/*.+(t|j)s?(x)`, { nodir: true })
-    )
+    const filesRegex = path.join(`/**`, `*.+(t|j)s?(x)`)
+    let files = [
+      path.join(this.base, `src`),
+      path.join(this.base, `.cache`, `fragments`),
+    ]
+      .concat(this.additional.map(additional => path.join(additional, `src`)))
+      .reduce(
+        (merged, folderPath) =>
+          merged.concat(
+            glob.sync(path.join(folderPath, filesRegex), {
+              nodir: true,
+            })
+          ),
+        []
+      )
     files = files.filter(d => !d.match(/\.d\.ts$/))
     files = files.map(normalize)
 
@@ -217,16 +233,13 @@ class Runner {
     return compiledNodes
   }
 }
-export { Runner }
+export { Runner, resolveThemes }
 
 export default async function compile(): Promise<Map<string, RootQuery>> {
-  const { program, schema } = store.getState()
+  // TODO: swap plugins to themes
+  const { program, schema, plugins } = store.getState()
 
-  const runner = new Runner(
-    `${program.directory}/src`,
-    `${program.directory}/.cache/fragments`,
-    schema
-  )
+  const runner = new Runner(program.directory, resolveThemes(plugins), schema)
 
   const queries = await runner.compileAll()