diff --git a/packages/core/src/cli/commands/init.command.ts b/packages/core/src/cli/commands/init.command.ts
index 73aa9dc8..7aa5240c 100644
--- a/packages/core/src/cli/commands/init.command.ts
+++ b/packages/core/src/cli/commands/init.command.ts
@@ -5,7 +5,7 @@ import { input, checkbox, confirm } from '@inquirer/prompts';
 import { tryCatch } from '@dmno/ts-lib';
 import Debug from 'debug';
 
-import { findDmnoServices } from '../../config-loader/find-services';
+import { findDmnoServices, selectAndApplyWorkspaceConfig } from '../../config-loader/find-services';
 import { DmnoCommand } from '../lib/dmno-command';
 
 import { joinAndCompact } from '../lib/formatting';
@@ -33,11 +33,13 @@ program.action(async (opts: {
   console.log(DMNO_DEV_BANNER);
   // console.log(kleur.gray('let us help you connect the dots ● ● ●'));
 
-  const [workspaceInfo] = await Promise.all([
+  const [workspaceInfoInitial] = await Promise.all([
     findDmnoServices(true),
     fallingDmnosAnimation(),
   ]);
 
+  // Handle workspace configuration selection after animation completes
+  const workspaceInfo = await selectAndApplyWorkspaceConfig(workspaceInfoInitial);
 
   // await fallingDmnoLoader('● Scanning repo', '● Scan complete');
 
diff --git a/packages/core/src/config-loader/config-loader.ts b/packages/core/src/config-loader/config-loader.ts
index f36bbb66..86f171d1 100644
--- a/packages/core/src/config-loader/config-loader.ts
+++ b/packages/core/src/config-loader/config-loader.ts
@@ -12,7 +12,7 @@ import { ViteNodeServer } from 'vite-node/server';
 import { createDeferredPromise } from '@dmno/ts-lib';
 import { createDebugTimer } from '../cli/lib/debug-timer';
 import { setupViteServer } from './vite-server';
-import { ScannedWorkspaceInfo, findDmnoServices } from './find-services';
+import { ScannedWorkspaceInfo, findDmnoServices, selectAndApplyWorkspaceConfig } from './find-services';
 import {
   DmnoService, DmnoWorkspace, DmnoServiceConfig,
 } from '../config-engine/config-engine';
@@ -55,7 +55,8 @@ export class ConfigLoader {
   }
 
   private async finishInit() {
-    this.workspaceInfo = await findDmnoServices();
+    const workspaceInfoInitial = await findDmnoServices();
+    this.workspaceInfo = await selectAndApplyWorkspaceConfig(workspaceInfoInitial);
     // already filtered to only services with a .dmno folder
     const dmnoServicePackages = this.workspaceInfo.workspacePackages;
 
diff --git a/packages/core/src/config-loader/find-services.ts b/packages/core/src/config-loader/find-services.ts
index 9586e5e4..1cb896f6 100644
--- a/packages/core/src/config-loader/find-services.ts
+++ b/packages/core/src/config-loader/find-services.ts
@@ -5,6 +5,7 @@ import readYamlFile from 'read-yaml-file';
 import { fdir } from 'fdir';
 import { tryCatch } from '@dmno/ts-lib';
 import Debug from 'debug';
+import { checkbox } from '@inquirer/prompts';
 import { pathExists } from '../lib/fs-utils';
 
 
@@ -41,6 +42,7 @@ export type ScannedWorkspaceInfo = {
   workspacePackages: Array<WorkspacePackagesListing>,
   autoSelectedPackage?: WorkspacePackagesListing,
   settings?: WorkspaceSettings,
+  workspaceConfigs?: WorkspaceConfigSource[],
 };
 
 // list of locations to look for workspace project globs
@@ -59,6 +61,13 @@ const WORKSPACE_SETTINGS_LOCATIONS = [
   // { file: 'deno.jsonc', path: 'workspace', optional: true },
 ];
 
+export type WorkspaceConfigSource = {
+  filePath: string;
+  settingsLocation: typeof WORKSPACE_SETTINGS_LOCATIONS[number];
+  packagePatterns: string[];
+  otherSettings?: WorkspaceSettings;
+};
+
 export async function findDmnoServices(includeUnitialized = false): Promise<ScannedWorkspaceInfo> {
   const startAt = new Date();
 
@@ -67,6 +76,7 @@ export async function findDmnoServices(includeUnitialized = false): Promise<Scan
   let dmnoWorkspaceFinal = false;
   let isMonorepo = false;
   let packagePatterns: Array<string> | undefined;
+  let workspaceConfigs: WorkspaceConfigSource[] = [];
 
   let otherSettings: WorkspaceSettings | undefined;
 
@@ -82,9 +92,12 @@ export async function findDmnoServices(includeUnitialized = false): Promise<Scan
         const filePath = path.join(cwd, settingsLocation.file);
         if (!await pathExists(filePath)) continue;
 
+        debug(`found workspace settings file: ${filePath}`);
+
         // assume first package.json file found is root until we find evidence otherwise
         if (settingsLocation.file === 'package.json' && !dmnoWorkspaceRootPath) {
           dmnoWorkspaceRootPath = cwd;
+          debug(`set dmnoWorkspaceRootPath to ${cwd} (from package.json)`);
         }
 
         debug(`looking for workspace globs in ${filePath} > ${settingsLocation.globsPath}`);
@@ -97,16 +110,38 @@ export async function findDmnoServices(includeUnitialized = false): Promise<Scan
         }
         const possiblePackagePatterns = _.get(fileContents, settingsLocation.globsPath);
         if (possiblePackagePatterns) {
-          packagePatterns = possiblePackagePatterns;
-          dmnoWorkspaceRootPath = cwd;
-          isMonorepo = true;
+          // Handle both legacy format (workspaces as array) and modern format (workspaces as object with packages property)
+          let actualPackagePatterns: string[] | undefined;
+          if (Array.isArray(possiblePackagePatterns)) {
+            actualPackagePatterns = possiblePackagePatterns;
+          } else if (possiblePackagePatterns && typeof possiblePackagePatterns === 'object' && possiblePackagePatterns.packages) {
+            actualPackagePatterns = possiblePackagePatterns.packages;
+          }
+          
+          if (actualPackagePatterns) {
+            debug(`found workspace patterns in ${filePath}:`, actualPackagePatterns);
+            
+            // Store this workspace configuration
+            workspaceConfigs.push({
+              filePath,
+              settingsLocation,
+              packagePatterns: actualPackagePatterns,
+              otherSettings: settingsLocation.file === '.dmno/workspace.yaml' ? _.omit(fileContents, settingsLocation.globsPath) : undefined
+            });
+            
+            // Set workspace root if not already set
+            if (!dmnoWorkspaceRootPath) {
+              dmnoWorkspaceRootPath = cwd;
+              debug(`updated dmnoWorkspaceRootPath to ${cwd} (from workspace patterns)`);
+            }
+            isMonorepo = true;
+          }
         }
 
         // if this is our dmno-specific file, we'll consider this "final" and stop scanning upwards
         if (settingsLocation.file === '.dmno/workspace.yaml') {
+          debug(`found dmno workspace config at ${filePath} - stopping upward scan`);
           dmnoWorkspaceFinal = true;
-          // everything else in the yaml file is additional settings
-          otherSettings = _.omit(fileContents, settingsLocation.globsPath);
           break; // breaks from for loop - will still continue looking for git root
         }
       }
@@ -131,6 +166,24 @@ export async function findDmnoServices(includeUnitialized = false): Promise<Scan
     throw new Error('Unable to detect dmno workspace root');
   }
 
+  // Process workspace configurations
+  if (workspaceConfigs.length > 0) {
+    // If there's only one config or they're all equivalent, select immediately
+    if (workspaceConfigs.length === 1 || areWorkspaceConfigsEquivalent(workspaceConfigs)) {
+      const selectedConfig = await selectWorkspaceConfig(workspaceConfigs);
+      packagePatterns = selectedConfig.packagePatterns;
+      if (selectedConfig.otherSettings) {
+        otherSettings = selectedConfig.otherSettings;
+      }
+    } else {
+      // Return the configs to be selected by the calling code
+      // Use the first config temporarily for the scanning phase
+      packagePatterns = workspaceConfigs[0].packagePatterns;
+      if (workspaceConfigs[0].otherSettings) {
+        otherSettings = workspaceConfigs[0].otherSettings;
+      }
+    }
+  }
 
   // const { packageManager, rootWorkspacePath: rootServicePath } = await detectPackageManager();
 
@@ -205,5 +258,161 @@ export async function findDmnoServices(includeUnitialized = false): Promise<Scan
     workspacePackages: includeUnitialized ? workspacePackages : _.filter(workspacePackages, (p) => p.dmnoFolder),
     autoSelectedPackage: packageFromPwd || packageFromCurrentPackageName,
     settings: otherSettings,
+    workspaceConfigs: workspaceConfigs.length > 1 && !areWorkspaceConfigsEquivalent(workspaceConfigs) ? workspaceConfigs : undefined,
+  };
+}
+
+function standardizePackagePatterns(patterns: string[]): string[] {
+  return _.uniq(patterns.map(p => p.trim()).filter(Boolean)).sort();
+}
+
+function areWorkspaceConfigsEquivalent(configs: WorkspaceConfigSource[]): boolean {
+  if (configs.length <= 1) return true;
+  
+  const standardizedPatterns = configs.map(config => 
+    standardizePackagePatterns(config.packagePatterns)
+  );
+  
+  const firstPatterns = standardizedPatterns[0];
+  return standardizedPatterns.every(patterns => 
+    _.isEqual(patterns, firstPatterns)
+  );
+}
+
+async function selectWorkspaceConfig(configs: WorkspaceConfigSource[]): Promise<{ packagePatterns: string[], otherSettings?: WorkspaceSettings }> {
+  if (configs.length === 0) {
+    throw new Error('No workspace configurations found');
+  }
+  
+  if (configs.length === 1) {
+    return {
+      packagePatterns: configs[0].packagePatterns,
+      otherSettings: configs[0].otherSettings
+    };
+  }
+  
+  // Check if all configurations are equivalent
+  if (areWorkspaceConfigsEquivalent(configs)) {
+    debug(`Found ${configs.length} workspace configurations, but they are equivalent - proceeding with first one`);
+    return {
+      packagePatterns: configs[0].packagePatterns,
+      otherSettings: configs[0].otherSettings
+    };
+  }
+  
+  // Check if we're in a non-interactive environment
+  const isNonInteractive = process.env.CI || process.env.TERM === 'dumb' || !process.stdin.isTTY;
+  
+  if (isNonInteractive) {
+    debug(`Found ${configs.length} different workspace configurations, using first one in non-interactive mode`);
+    debug(`Selected: ${configs[0].filePath} - ${configs[0].packagePatterns.join(', ')}`);
+    return {
+      packagePatterns: configs[0].packagePatterns,
+      otherSettings: configs[0].otherSettings
+    };
+  }
+  
+  // Show user selection for different configurations
+  const selectedConfigIndices = await checkbox({
+    message: `Found ${configs.length} different workspace configurations.\nSelect which to use (Press <space> to select, <a> to toggle all, <enter> to proceed):\n`,
+    choices: configs.map((config, index) => ({
+      name: `${config.filePath} - [${config.packagePatterns.join(', ')}]`,
+      value: index,
+      checked: index === 0 // Default to first one
+    })),
+    instructions: false
+  });
+  
+  if (selectedConfigIndices.length === 0) {
+    throw new Error('No workspace configuration selected');
+  }
+  
+  // Combine selected configurations and deduplicate
+  const selectedConfigs = selectedConfigIndices.map(index => configs[index]);
+  const allPatterns = _.flatten(selectedConfigs.map(config => config.packagePatterns));
+  const deduplicatedPatterns = standardizePackagePatterns(allPatterns);
+  
+  // Merge other settings from selected configs
+  const mergedOtherSettings = selectedConfigs.reduce((acc, config) => {
+    if (config.otherSettings) {
+      return _.merge(acc, config.otherSettings);
+    }
+    return acc;
+  }, {} as WorkspaceSettings);
+  
+  debug(`Selected ${selectedConfigs.length} workspace configurations, deduplicated to ${deduplicatedPatterns.length} patterns`);
+  
+  return {
+    packagePatterns: deduplicatedPatterns,
+    otherSettings: Object.keys(mergedOtherSettings).length > 0 ? mergedOtherSettings : undefined
+  };
+}
+
+export async function selectAndApplyWorkspaceConfig(workspaceInfo: ScannedWorkspaceInfo): Promise<ScannedWorkspaceInfo> {
+  if (!workspaceInfo.workspaceConfigs || workspaceInfo.workspaceConfigs.length <= 1) {
+    return workspaceInfo;
+  }
+
+  const selectedConfig = await selectWorkspaceConfig(workspaceInfo.workspaceConfigs);
+  
+  // Get the workspace root path from the original info
+  const dmnoWorkspaceRootPath = workspaceInfo.workspacePackages.find(p => p.isRoot)?.path;
+  if (!dmnoWorkspaceRootPath) {
+    throw new Error('Unable to find workspace root path');
+  }
+  
+  // Rebuild package paths with selected patterns
+  let packagePaths = [dmnoWorkspaceRootPath];
+  if (workspaceInfo.isMonorepo && selectedConfig.packagePatterns?.length) {
+    const fullPackagePatterns = selectedConfig.packagePatterns.map((gi) => path.join(dmnoWorkspaceRootPath, gi));
+    const patternsByType = _.groupBy(
+      fullPackagePatterns,
+      (s) => (s.includes('*') ? 'globs' : 'dirs'),
+    );
+
+    const expandedPathsFromGlobs = await (
+      new fdir()
+        .withBasePath()
+        .onlyDirs()
+        .glob(...patternsByType.globs || [])
+        .exclude((dirName, _dirPath) => {
+          return dirName === 'node_modules';
+        })
+        .crawl(dmnoWorkspaceRootPath)
+        .withPromise()
+    );
+    packagePaths.push(...patternsByType.dirs || []);
+    packagePaths.push(...expandedPathsFromGlobs);
+    packagePaths = packagePaths.map((p) => p.replace(/\/$/, ''));
+    packagePaths = _.uniq(packagePaths);
+  }
+
+  // Rebuild workspace packages
+  const workspacePackages = _.compact(await Promise.all(packagePaths.map(async (packagePath) => {
+    const packageJson = await tryCatch(
+      async () => await readJsonFile(path.join(packagePath, 'package.json')),
+      (err) => {
+        if ((err as any).code === 'ENOENT') return undefined;
+        throw err;
+      },
+    );
+
+    const dmnoFolderExists = await pathExists(path.join(packagePath, '.dmno'));
+    const packageName = packageJson?.name || packagePath.split('/').pop();
+
+    return {
+      isRoot: packagePath === dmnoWorkspaceRootPath,
+      path: packagePath,
+      relativePath: packagePath.substring(dmnoWorkspaceRootPath.length + 1),
+      name: packageName,
+      dmnoFolder: dmnoFolderExists,
+    };
+  })));
+
+  return {
+    ...workspaceInfo,
+    workspacePackages,
+    settings: selectedConfig.otherSettings || workspaceInfo.settings,
+    workspaceConfigs: undefined // Clear this since we've made the selection
   };
 }