diff --git a/lib/CourseThemeModule.js b/lib/CourseThemeModule.js
index d943b3e..9261378 100644
--- a/lib/CourseThemeModule.js
+++ b/lib/CourseThemeModule.js
@@ -1,7 +1,11 @@
 import _ from 'lodash'
 import AbstractApiModule from 'adapt-authoring-api'
 import fs from 'fs/promises'
+import semver from 'semver'
 import { getVariablesString, processCustomStyling } from './utils.js'
+
+const CONFIG_THEME_VARS_MIN_VERSION = '6.61.0' // adjust to actual release version
+
 /**
  * Module which handles course theming
  * @memberof coursetheme
@@ -26,7 +30,22 @@ class CourseThemeModule extends AbstractApiModule {
      * @type {ContentModule}
      */
     this.content = content
+    /**
+     * Cached module instance for easy access
+     * @type {AdaptFrameworkModule}
+     */
+    this.framework = framework
     framework.preBuildHook.tap(this.writeCustomLess.bind(this))
+    framework.registerImportContentMigration(async (data, importer) => {
+      if (data._type === 'course' && data.themeVariables) {
+        importer._themeVariablesMigration = data.themeVariables
+        delete data.themeVariables
+      }
+      if (data._type === 'config' && importer._themeVariablesMigration) {
+        data.themeVariables = importer._themeVariablesMigration
+        delete importer._themeVariablesMigration
+      }
+    })
   }
 
   /**
@@ -34,12 +53,20 @@ class CourseThemeModule extends AbstractApiModule {
    * @param {AdaptFrameworkBuild} fwBuild Reference to the current build
    */
   async writeCustomLess (fwBuild) {
-    const fontImportString = await this.processFileVariables(fwBuild)
-    processCustomStyling(fwBuild.courseData)
+    const configData = fwBuild.courseData.config.data
+    const courseData = fwBuild.courseData.course.data
+    // prefer config, fall back to course for unmigrated data
+    const variables = configData[this.attributeKey] || courseData[this.attributeKey] || {}
+
+    const fontImportString = await this.processFileVariables(fwBuild, variables)
+    processCustomStyling(fwBuild.courseData, variables)
+
+    const { customStyle, themeCustomStyle } = courseData
+    const frameworkHandlesVars = semver.gte(this.framework.version, CONFIG_THEME_VARS_MIN_VERSION)
 
-    const { customStyle, [this.attributeKey]: variables, themeCustomStyle } = fwBuild.courseData.course.data
     return Promise.all([
-      this.writeFile(fwBuild, '1-variables.less', fontImportString + getVariablesString(variables)),
+      this.writeFile(fwBuild, '1-variables.less',
+        frameworkHandlesVars ? fontImportString : fontImportString + getVariablesString(variables)),
       this.writeFile(fwBuild, '2-customStyles.less', customStyle),
       this.writeFile(fwBuild, '3-themeCustomStyles.less', themeCustomStyle)
     ])
@@ -74,8 +101,9 @@ class CourseThemeModule extends AbstractApiModule {
   async applyHandler (req, res, next) {
     try {
       const { _id, courseId } = req.apiData.query
-      const [{ properties: presetProps }] = await this.find({ _id })
-      await this.content.update({ _id: courseId }, { [this.attributeKey]: presetProps })
+      const { properties: presetProps } = await this.findOne({ _id })
+      const config = await this.content.findOne({ _courseId: courseId, _type: 'config' })
+      await this.content.update({ _id: config._id }, { [this.attributeKey]: presetProps })
       res.sendStatus(204)
     } catch (e) {
       return next(e)
@@ -91,9 +119,10 @@ class CourseThemeModule extends AbstractApiModule {
   async removeHandler (req, res, next) {
     try {
       const { _id, courseId } = req.apiData.query
-      const [{ properties: presetProps }] = await this.find({ _id })
-      const [{ themeVariables: existingProps }] = await this.content.find({ _id: courseId })
-      await this.content.update({ _id: courseId }, { [this.attributeKey]: _.pickBy(existingProps, (v, k) => v !== presetProps[k]) })
+      const { properties: presetProps } = await this.findOne({ _id })
+      const config = await this.content.findOne({ _courseId: courseId, _type: 'config' })
+      const existingProps = config[this.attributeKey] || {}
+      await this.content.update({ _id: config._id }, { [this.attributeKey]: _.pickBy(existingProps, (v, k) => v !== presetProps[k]) })
       res.sendStatus(204)
     } catch (e) {
       return next(e)
@@ -102,11 +131,12 @@ class CourseThemeModule extends AbstractApiModule {
 
   /**
    * Copies uploaded font files into the build
-   * @param {object} data The data to process
+   * @param {AdaptFrameworkBuild} fwBuild Reference to the current build
+   * @param {Object} variables The theme variables object
    */
-  async processFileVariables (fwBuild) {
+  async processFileVariables (fwBuild, variables) {
     const assets = await this.app.waitForModule('assets')
-    const fontData = fwBuild.courseData.course.data.themeVariables._font
+    const fontData = variables?._font
 
     if (!fontData) {
       return ''
@@ -118,7 +148,7 @@ class CourseThemeModule extends AbstractApiModule {
         if (!f['font-family']) return
         // copy each uploaded font file
         for (const font in f._files) {
-          const [data] = await assets.find({ _id: f._files[font] })
+          const data = await assets.findOne({ _id: f._files[font] })
           const asset = assets.createFsWrapper(data)
           try {
             const relativeFontPath = `fonts/${f._files[font]}.${asset.data.subtype}`
diff --git a/lib/utils/processCustomStyling.js b/lib/utils/processCustomStyling.js
index 4509634..9ebd441 100644
--- a/lib/utils/processCustomStyling.js
+++ b/lib/utils/processCustomStyling.js
@@ -2,14 +2,15 @@
  * Processes custom styling by moving the themeCustomStyle attribute from
  * themeVariables to the top-level course data
  * @param {Object} courseData The course data object (fwBuild.courseData)
+ * @param {Object} variables The theme variables object
  * @memberof coursetheme
  */
-export function processCustomStyling (courseData) {
-  const customStyling = courseData.course.data.themeVariables.themeCustomStyle
+export function processCustomStyling (courseData, variables) {
+  const customStyling = variables?.themeCustomStyle
 
   if (!customStyling) return
 
   courseData.course.data.themeCustomStyle = customStyling
 
-  delete courseData.course.data.themeVariables.themeCustomStyle
+  delete variables.themeCustomStyle
 }
diff --git a/package.json b/package.json
index d82f076..dd9d4f0 100644
--- a/package.json
+++ b/package.json
@@ -9,7 +9,8 @@
   "repository": "github:adapt-security/adapt-authoring-coursetheme",
   "dependencies": {
     "adapt-authoring-api": "^3.0.0",
-    "lodash": "^4.17.21"
+    "lodash": "^4.17.21",
+    "semver": "^7.6.0"
   },
   "peerDependencies": {
     "adapt-authoring-adaptframework": "^2.0.0",