diff --git a/cmd/docker-mcp/commands/workingset.go b/cmd/docker-mcp/commands/workingset.go
index f30576cf..c1381a93 100644
--- a/cmd/docker-mcp/commands/workingset.go
+++ b/cmd/docker-mcp/commands/workingset.go
@@ -63,7 +63,7 @@ func configWorkingSetCommand() *cobra.Command {
 	}
 
 	flags := cmd.Flags()
-	flags.StringArrayVar(&set, "set", []string{}, "Set configuration values: <key>=<value> (can be specified multiple times)")
+	flags.StringArrayVar(&set, "set", []string{}, "Set configuration values: <key>=<value> (repeatable). Value may be JSON to set typed values (arrays, numbers, booleans, objects).")
 	flags.StringArrayVar(&get, "get", []string{}, "Get configuration values: <key> (can be specified multiple times)")
 	flags.StringArrayVar(&del, "del", []string{}, "Delete configuration values: <key> (can be specified multiple times)")
 	flags.BoolVar(&getAll, "get-all", false, "Get all configuration values")
diff --git a/docs/profiles.md b/docs/profiles.md
index 8314c1c7..decc22ae 100644
--- a/docs/profiles.md
+++ b/docs/profiles.md
@@ -270,6 +270,27 @@ docker mcp profile config my-profile --get-all --format yaml
 - `--get-all`: Retrieves all configuration values from all servers in the profile
 - `--format`: Output format - `human` (default), `json`, or `yaml`
 
+**Typed values via JSON:**
+
+- Values passed to `--set` are parsed as JSON when possible. This allows arrays, numbers, booleans and objects.
+- If the value is not valid JSON, it is stored as a plain string.
+- Examples:
+
+```bash
+# Numbers and booleans
+docker mcp profile config my-profile --set github.timeout=60 --set github.debug=true
+
+# Strings (either raw or JSON-quoted both work)
+docker mcp profile config my-profile --set slack.channel=general
+docker mcp profile config my-profile --set slack.channel='"general"'
+
+# Arrays
+docker mcp profile config my-profile --set filesystem.paths='["/Users/dk/dev","/Users/dk/projects"]'
+
+# Objects
+docker mcp profile config my-profile --set build.options='{"retries":3,"cache":false}'
+```
+
 **Important notes:**
 - The server name must match the name from the server's snapshot (not the image or source URL)
 - Use `docker mcp profile show <profile-id> --format yaml` to see available server names
diff --git a/pkg/workingset/config.go b/pkg/workingset/config.go
index 0dd2d07b..96867231 100644
--- a/pkg/workingset/config.go
+++ b/pkg/workingset/config.go
@@ -39,12 +39,12 @@ func UpdateConfig(ctx context.Context, dao db.DAO, ociService oci.Service, id st
 		return fmt.Errorf("failed to resolve snapshots: %w", err)
 	}
 
-	outputMap := make(map[string]string)
+	outputMap := make(map[string]any)
 
 	if getAll {
 		for _, server := range workingSet.Servers {
 			for configName, value := range server.Config {
-				outputMap[fmt.Sprintf("%s.%s", server.Snapshot.Server.Name, configName)] = fmt.Sprintf("%v", value)
+				outputMap[fmt.Sprintf("%s.%s", server.Snapshot.Server.Name, configName)] = value
 			}
 		}
 	} else {
@@ -60,7 +60,7 @@ func UpdateConfig(ctx context.Context, dao db.DAO, ociService oci.Service, id st
 			}
 
 			if server.Config != nil && server.Config[configName] != nil {
-				outputMap[configArg] = fmt.Sprintf("%v", server.Config[configName])
+				outputMap[configArg] = server.Config[configName]
 			}
 		}
 	}
@@ -84,9 +84,14 @@ func UpdateConfig(ctx context.Context, dao db.DAO, ociService oci.Service, id st
 		if server.Config == nil {
 			server.Config = make(map[string]any)
 		}
-		// TODO(cody): validate that schema supports the config we're adding and map it to the right type (right now we're forcing a string)
-		server.Config[configName] = value
-		outputMap[key] = value
+		// TODO(cody): validate that schema supports the config we're adding
+		finalValue := any(value)
+		var decoded any
+		if err := json.Unmarshal([]byte(value), &decoded); err == nil {
+			finalValue = decoded
+		}
+		server.Config[configName] = finalValue
+		outputMap[key] = finalValue
 	}
 
 	for _, delConfigArg := range delConfigArgs {
@@ -116,7 +121,7 @@ func UpdateConfig(ctx context.Context, dao db.DAO, ociService oci.Service, id st
 	switch outputFormat {
 	case OutputFormatHumanReadable:
 		for configName, value := range outputMap {
-			fmt.Printf("%s=%s\n", configName, value)
+			fmt.Printf("%s=%v\n", configName, value)
 		}
 	case OutputFormatJSON:
 		data, err := json.MarshalIndent(outputMap, "", "  ")
diff --git a/pkg/workingset/config_test.go b/pkg/workingset/config_test.go
index 79377fcc..f6427358 100644
--- a/pkg/workingset/config_test.go
+++ b/pkg/workingset/config_test.go
@@ -92,8 +92,8 @@ func TestUpdateConfig_SetMultipleValues(t *testing.T) {
 	dbSet, err := dao.GetWorkingSet(ctx, "test-set")
 	require.NoError(t, err)
 	assert.Equal(t, "secret123", dbSet.Servers[0].Config["api_key"])
-	assert.Equal(t, "30", dbSet.Servers[0].Config["timeout"])
-	assert.Equal(t, "true", dbSet.Servers[0].Config["enabled"])
+	assert.Equal(t, 30, int(dbSet.Servers[0].Config["timeout"].(float64)))
+	assert.Equal(t, true, dbSet.Servers[0].Config["enabled"])
 }
 
 func TestUpdateConfig_GetSingleValue(t *testing.T) {
@@ -356,6 +356,57 @@ func TestUpdateConfig_YAMLOutput(t *testing.T) {
 	assert.Equal(t, "secret123", result["test-server.api_key"])
 }
 
+func TestUpdateConfig_JSONOutput_TypedArray(t *testing.T) {
+	dao := setupTestDB(t)
+	ctx := t.Context()
+
+	err := dao.CreateWorkingSet(ctx, db.WorkingSet{
+		ID:   "test-set",
+		Name: "Test Working Set",
+		Servers: db.ServerList{
+			{
+				Type:  "image",
+				Image: "myimage:latest",
+				Snapshot: &db.ServerSnapshot{
+					Server: catalog.Server{
+						Name: "filesystem",
+					},
+				},
+			},
+		},
+		Secrets: db.SecretMap{},
+	})
+	require.NoError(t, err)
+
+	ociService := getMockOciService()
+
+	// Set typed array value
+	_ = captureStdout(func() {
+		err = UpdateConfig(ctx, dao, ociService, "test-set",
+			[]string{`filesystem.paths=["/Users/dk/dev","/Users/dk/projects"]`},
+			[]string{}, []string{}, false, OutputFormatHumanReadable)
+		require.NoError(t, err)
+	})
+
+	// Get JSON, ensure array is preserved as array
+	output := captureStdout(func() {
+		err = UpdateConfig(ctx, dao, ociService, "test-set",
+			[]string{}, []string{"filesystem.paths"}, []string{}, false, OutputFormatJSON)
+		require.NoError(t, err)
+	})
+
+	var result map[string]any
+	err = json.Unmarshal([]byte(output), &result)
+	require.NoError(t, err)
+
+	raw := result["filesystem.paths"]
+	list, ok := raw.([]any)
+	require.True(t, ok)
+	require.Len(t, list, 2)
+	assert.Equal(t, "/Users/dk/dev", list[0].(string))
+	assert.Equal(t, "/Users/dk/projects", list[1].(string))
+}
+
 func TestUpdateConfig_WorkingSetNotFound(t *testing.T) {
 	dao := setupTestDB(t)
 	ctx := t.Context()