diff --git a/package-lock.json b/package-lock.json
index d4273da..e748094 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -35,11 +35,12 @@
         "release-it": "^14.13.1",
         "rimraf": "^3.0.2",
         "rollup": "^2.70.1",
+        "rollup-plugin-multi-input": "^1.3.1",
         "semver": "^7.3.5",
         "typescript": "^4.6.2"
       },
       "engines": {
-        "node": ">=16.0.0"
+        "node": ">=14"
       }
     },
     "node_modules/@ampproject/remapping": {
@@ -13939,6 +13940,17 @@
         "yarn": ">=1.0.0"
       }
     },
+    "node_modules/rollup-plugin-multi-input": {
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/rollup-plugin-multi-input/-/rollup-plugin-multi-input-1.3.1.tgz",
+      "integrity": "sha512-bPsxHR6dUney7zsCAAlfkq7lbuy5xph2CvUstSv88oqhtRiLWXwVjiA1Gb4HVjC6I9sJI2eZeQlozXa+GXJKDA==",
+      "dev": true,
+      "dependencies": {
+        "core-js": "^3.1.3",
+        "fast-glob": "^3.0.0",
+        "lodash": "^4.17.11"
+      }
+    },
     "node_modules/rollup-plugin-rebase": {
       "version": "4.0.1",
       "resolved": "https://registry.npmjs.org/rollup-plugin-rebase/-/rollup-plugin-rebase-4.0.1.tgz",
@@ -26668,6 +26680,17 @@
         "@babel/runtime": "^7.14.0"
       }
     },
+    "rollup-plugin-multi-input": {
+      "version": "1.3.1",
+      "resolved": "https://registry.npmjs.org/rollup-plugin-multi-input/-/rollup-plugin-multi-input-1.3.1.tgz",
+      "integrity": "sha512-bPsxHR6dUney7zsCAAlfkq7lbuy5xph2CvUstSv88oqhtRiLWXwVjiA1Gb4HVjC6I9sJI2eZeQlozXa+GXJKDA==",
+      "dev": true,
+      "requires": {
+        "core-js": "^3.1.3",
+        "fast-glob": "^3.0.0",
+        "lodash": "^4.17.11"
+      }
+    },
     "rollup-plugin-rebase": {
       "version": "4.0.1",
       "resolved": "https://registry.npmjs.org/rollup-plugin-rebase/-/rollup-plugin-rebase-4.0.1.tgz",
diff --git a/package.json b/package.json
index 2a823ae..400aec5 100644
--- a/package.json
+++ b/package.json
@@ -61,6 +61,7 @@
     "release-it": "^14.13.1",
     "rimraf": "^3.0.2",
     "rollup": "^2.70.1",
+    "rollup-plugin-multi-input": "^1.3.1",
     "semver": "^7.3.5",
     "typescript": "^4.6.2"
   }
diff --git a/src/index.js b/src/index.js
index 05bb427..8196d8e 100644
--- a/src/index.js
+++ b/src/index.js
@@ -11,6 +11,8 @@ import postcssSugarSS from "sugarss"
 import { createFilter } from "@rollup/pluginutils"
 import { getHash } from "asset-hash"
 
+const MULTI_INPUT_PLUGIN_NAME = 'rollup-plugin-multi-input'
+
 const scriptExtensions = /^\.(json|mjs|js|jsx|ts|tsx)$/
 
 const styleParser = {
@@ -27,7 +29,7 @@ function getPostCssPlugins(keepName) {
     postcssSmartAsset({
       url: "copy",
       useHash: true,
-      keepName
+      keepName,
     })
   ]
 }
@@ -61,7 +63,7 @@ export default function rebase(options = {}) {
     exclude,
     verbose = false,
     keepName = false,
-    assetFolder = ""
+    assetFolder = "",
   } = options
 
   const filter = createFilter(include, exclude)
@@ -70,6 +72,7 @@ export default function rebase(options = {}) {
   const files = {}
 
   let root = null
+  let hasMultiInput = false
 
   function rootRelative(file) {
     // Last sequence is for Windows support
@@ -94,12 +97,20 @@ export default function rebase(options = {}) {
       return Boolean(files[fileSource])
     },
 
+    options({ plugins }) {
+      // Check whether we are using rollup-plugin-multi-input
+      hasMultiInput = !!plugins?.some(plugin => plugin != null && typeof plugin !== "boolean" && plugin.name === MULTI_INPUT_PLUGIN_NAME)
+    },
+
     /* eslint-disable complexity, max-statements */
     async resolveId(importee, importer) {
       // Ignore root files which are typically script files. Delegate to other
       // plugins or default behavior.
       if (!importer) {
-        root = path.dirname(path.resolve(importee))
+        // If multiInput is detected, set root once for proper paths
+        if (!hasMultiInput || (hasMultiInput && !root)) {
+          root = path.dirname(path.resolve(importee))
+        }
         return null
       }
 
diff --git a/test/multi-input/__snapshots__/index.test.js.snap b/test/multi-input/__snapshots__/index.test.js.snap
new file mode 100644
index 0000000..e87d4d1
--- /dev/null
+++ b/test/multi-input/__snapshots__/index.test.js.snap
@@ -0,0 +1,28 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`Multi input support 1`] = `
+"HDWIGpiP.md
+SmVOQyTt.png
+index.js
+sub"
+`;
+
+exports[`Multi input support 2`] = `
+"import index from './sub/folder/child.js';
+export { default } from './sub/folder/child.js';
+import './SmVOQyTt.png';
+import './HDWIGpiP.md';
+"
+`;
+
+exports[`Multi input support 3`] = `
+"import image from '../../SmVOQyTt.png';
+import content from '../../HDWIGpiP.md';
+
+function index() {
+  return content + image
+}
+
+export { index as default };
+"
+`;
diff --git a/test/multi-input/index.test.js b/test/multi-input/index.test.js
new file mode 100644
index 0000000..9271197
--- /dev/null
+++ b/test/multi-input/index.test.js
@@ -0,0 +1,19 @@
+import { bundleWithMultiInput, clean, list, read } from "../util"
+import { join, sep } from "path"
+
+const root = __dirname
+
+test("Multi input support", async () => {
+  await bundleWithMultiInput(root, ['src/**/!(*.test).js'], "output", {}, {
+    transformOutputPath: (output) => {
+      // Need to transform output as bundle path starts from root of project
+      return output.replace(`${join('test', 'multi-input', 'src')}${sep}`, '');
+    },
+  })
+
+  expect(await list(root, "output")).toMatchSnapshot()
+  expect(await read(root, "output/index.js")).toMatchSnapshot()
+  expect(await read(root, "output/sub/folder/child.js")).toMatchSnapshot()
+
+  await clean(root, "output")
+})
diff --git a/test/multi-input/src/image.png b/test/multi-input/src/image.png
new file mode 100644
index 0000000..c5916f2
Binary files /dev/null and b/test/multi-input/src/image.png differ
diff --git a/test/multi-input/src/index.js b/test/multi-input/src/index.js
new file mode 100644
index 0000000..aa0734b
--- /dev/null
+++ b/test/multi-input/src/index.js
@@ -0,0 +1,3 @@
+import index from "./sub/folder/child"
+
+export default index
diff --git a/test/multi-input/src/sub/folder/child.js b/test/multi-input/src/sub/folder/child.js
new file mode 100644
index 0000000..7b67167
--- /dev/null
+++ b/test/multi-input/src/sub/folder/child.js
@@ -0,0 +1,6 @@
+import image from "../../image.png"
+import content from "./content.md"
+
+export default function() {
+  return content + image
+}
diff --git a/test/multi-input/src/sub/folder/content.md b/test/multi-input/src/sub/folder/content.md
new file mode 100644
index 0000000..fec5601
--- /dev/null
+++ b/test/multi-input/src/sub/folder/content.md
@@ -0,0 +1 @@
+# Hello
diff --git a/test/util.js b/test/util.js
index 00c3b52..9665ca3 100644
--- a/test/util.js
+++ b/test/util.js
@@ -3,6 +3,7 @@ import { readdir } from "fs"
 
 import fs from "fs-extra"
 import { rollup } from "rollup"
+import multiInput from "rollup-plugin-multi-input";
 
 import rebasePlugin from "../src"
 
@@ -21,6 +22,23 @@ export async function bundle(root, input, output, pluginOptions = {}) {
   })
 }
 
+export async function bundleWithMultiInput(root, input, output, pluginOptions = {}, multiInputOptions = {}) {
+  const plugins = [
+    multiInput(multiInputOptions),
+    rebasePlugin(pluginOptions)
+  ];
+
+  const result = await rollup({
+    input: input.map(i => join(root, i)),
+    plugins,
+  })
+
+  await result.write({
+    format: "es",
+    dir: join(root, output),
+  })
+}
+
 export async function clean(root, files) {
   const input = Array.isArray(files) ? files : [ files ]
   const tasks = input.map((file) => fs.remove(join(root, file)))