diff --git a/app/cli/cmd/root.go b/app/cli/cmd/root.go
index 598cf8881..ace1da2a8 100644
--- a/app/cli/cmd/root.go
+++ b/app/cli/cmd/root.go
@@ -398,7 +398,7 @@ func cleanup(conn *grpc.ClientConn) error {
 // 2. If the command does not require an API token, we
 // 2.1 Return the token explicitly provided via the flag
 // 2.2 Load the token from the environment variable and from the auth login config file
-// 2.3 if they both exist, we default to the user token
+// 2.3 if they both exist, we default to the API token from the environment variable
 // 2.4 otherwise to the one that's set
 func loadAuthToken(cmd *cobra.Command) (string, bool, error) {
 	// Load the APIToken from the env variable
@@ -423,11 +423,13 @@ func loadAuthToken(cmd *cobra.Command) (string, bool, error) {
 		return apiToken, false, nil
 	}
 
-	// If both the user authentication and the API token en var are set, we default to user authentication
-	if userToken != "" && apiTokenFromVar != "" {
-		logger.Warn().Msgf("Both user credentials and $%s set. Ignoring $%s.", tokenEnvVarName, tokenEnvVarName)
-		return userToken, true, nil
-	} else if apiTokenFromVar != "" {
+	// If the API token env var is set we default to it. An explicitly exported $CHAINLOOP_TOKEN is a
+	// stronger signal of intent than a (possibly stale) login session, and API tokens can now perform
+	// the same operations as user credentials. We warn if user credentials are also present.
+	if apiTokenFromVar != "" {
+		if userToken != "" {
+			logger.Warn().Msgf("Both user credentials and $%s set. Ignoring user credentials.", tokenEnvVarName)
+		}
 		return apiTokenFromVar, false, nil
 	}
 
diff --git a/app/cli/cmd/root_test.go b/app/cli/cmd/root_test.go
new file mode 100644
index 000000000..8799c7fa1
--- /dev/null
+++ b/app/cli/cmd/root_test.go
@@ -0,0 +1,113 @@
+// Copyright 2024-2026 The Chainloop Authors.
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+
+package cmd
+
+import (
+	"testing"
+
+	"github.com/spf13/cobra"
+	"github.com/spf13/viper"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+)
+
+func TestLoadAuthToken(t *testing.T) {
+	const (
+		envToken  = "env-token"
+		userTok   = "user-token"
+		flagToken = "flag-token"
+	)
+
+	testCases := []struct {
+		name string
+		// inputs
+		envVar         string
+		userToken      string
+		flag           string
+		apiTokenPref   bool
+		expectedToken  string
+		expectedIsUser bool
+	}{
+		{
+			name:           "only env var set, non API-preferred command",
+			envVar:         envToken,
+			expectedToken:  envToken,
+			expectedIsUser: false,
+		},
+		{
+			name:           "only user token set",
+			userToken:      userTok,
+			expectedToken:  userTok,
+			expectedIsUser: true,
+		},
+		{
+			name:           "both set, command does not prefer API token, env var wins",
+			envVar:         envToken,
+			userToken:      userTok,
+			apiTokenPref:   false,
+			expectedToken:  envToken,
+			expectedIsUser: false,
+		},
+		{
+			name:           "both set, command prefers API token, env var wins",
+			envVar:         envToken,
+			userToken:      userTok,
+			apiTokenPref:   true,
+			expectedToken:  envToken,
+			expectedIsUser: false,
+		},
+		{
+			name:           "flag takes precedence over env var and user token",
+			envVar:         envToken,
+			userToken:      userTok,
+			flag:           flagToken,
+			expectedToken:  flagToken,
+			expectedIsUser: false,
+		},
+		{
+			name:           "nothing set returns empty user token",
+			expectedToken:  "",
+			expectedIsUser: true,
+		},
+	}
+
+	for _, tc := range testCases {
+		t.Run(tc.name, func(t *testing.T) {
+			// Reset and set up the global state the function relies on
+			viper.Reset()
+			t.Cleanup(viper.Reset)
+			viper.Set(confOptions.authToken.viperKey, tc.userToken)
+
+			if tc.envVar != "" {
+				t.Setenv(tokenEnvVarName, tc.envVar)
+			}
+
+			// apiToken is a package-level variable bound to the --token flag
+			prevAPIToken := apiToken
+			apiToken = tc.flag
+			t.Cleanup(func() { apiToken = prevAPIToken })
+
+			cmd := &cobra.Command{Annotations: map[string]string{}}
+			if tc.apiTokenPref {
+				cmd.Annotations[useAPIToken] = trueString
+			}
+
+			got, isUser, err := loadAuthToken(cmd)
+			require.NoError(t, err)
+			assert.Equal(t, tc.expectedToken, got)
+			assert.Equal(t, tc.expectedIsUser, isUser)
+		})
+	}
+}