diff --git a/core/bootstrap.go b/core/bootstrap.go
index f8dcf9ff2e..df4933e771 100644
--- a/core/bootstrap.go
+++ b/core/bootstrap.go
@@ -236,7 +236,12 @@ func Bootstrap(config *BootstrapConfig) (exitCode int, result any, err error) {
 	// Run checks after command has been executed
 	defer func() { // if we plan to remove defer, do not forget logger is not set until cobra pre init func
 		// Check CLI new version and api key expiration date
-		runAfterCommandChecks(ctx, config.BuildInfo.checkVersion, checkAPIKey)
+		runAfterCommandChecks(
+			ctx,
+			config.BuildInfo.checkVersion,
+			checkAPIKey,
+			checkIfMultipleVariableSources,
+		)
 	}()
 
 	if !config.DisableAliases {
diff --git a/core/checks.go b/core/checks.go
index 6f257c6f0b..e17f6d4f15 100644
--- a/core/checks.go
+++ b/core/checks.go
@@ -1,13 +1,16 @@
 package core
 
 import (
+	"bytes"
 	"context"
 	"fmt"
 	"os"
 	"path/filepath"
+	"reflect"
 	"time"
 
 	iam "github.com/scaleway/scaleway-sdk-go/api/iam/v1alpha1"
+	"github.com/scaleway/scaleway-sdk-go/scw"
 )
 
 var (
@@ -15,6 +18,10 @@ var (
 	lastChecksFileLocalName = "last-cli-checks"
 )
 
+const (
+	defaultCredentialSource = "environment variable"
+)
+
 type AfterCommandCheckFunc func(ctx context.Context)
 
 // wasFileModifiedLast24h checks whether the file has been updated during last 24 hours.
@@ -105,3 +112,43 @@ func checkAPIKey(ctx context.Context) {
 		ExtractLogger(ctx).Warningf("Current api key expires in %s\n", expiresIn)
 	}
 }
+
+// checkIfMultipleVariableSources return an informative message during the CLI initialization
+// if there are multiple sources of configuration that could confuse the user
+func checkIfMultipleVariableSources(ctx context.Context) {
+	config, err := scw.LoadConfigFromPath(ExtractConfigPath(ctx))
+	if err != nil {
+		return
+	}
+
+	activeProfile, err := config.GetActiveProfile()
+	if err != nil {
+		return
+	}
+
+	profileEnv := scw.LoadEnvProfile()
+
+	vFile := reflect.ValueOf(activeProfile).Elem()
+	vEnv := reflect.ValueOf(profileEnv).Elem()
+	t := vFile.Type()
+
+	var buffer bytes.Buffer
+	buffer.WriteString("Checking multiple variable sources: \n")
+
+	for i := range t.NumField() {
+		valFile := vFile.Field(i)
+		valEnv := vEnv.Field(i)
+
+		if !valFile.IsNil() && !valEnv.IsNil() {
+			if valFile.Elem().String() != valEnv.Elem().String() {
+				buffer.WriteString(fmt.Sprintf(
+					"- Variable '%s' is defined in both config.yaml and environment with different values. Using: %s.\n",
+					t.Field(i).Name,
+					defaultCredentialSource,
+				))
+			}
+		}
+	}
+
+	ExtractLogger(ctx).Warning(buffer.String())
+}
diff --git a/core/checks_test.go b/core/checks_test.go
index 58a2681d6b..6470e8c76f 100644
--- a/core/checks_test.go
+++ b/core/checks_test.go
@@ -86,3 +86,54 @@ func TestCheckAPIKey(t *testing.T) {
 		},
 	}))
 }
+
+func TestCheckIfMultipleVariableSources(t *testing.T) {
+	testCommands := core.NewCommands(
+		&core.Command{
+			Namespace: "test",
+			ArgSpecs:  core.ArgSpecs{},
+			ArgsType:  reflect.TypeOf(testType{}),
+			Run:       func(ctx context.Context, _ any) (any, error) { return "", nil },
+		},
+	)
+
+	t.Run("conflicting sources should trigger warning", core.Test(&core.TestConfig{
+		Commands:   testCommands,
+		TmpHomeDir: true,
+		BeforeFunc: func(ctx *core.BeforeFuncCtx) error {
+			cfg := &scw.Config{
+				Profile: scw.Profile{
+					AccessKey:        scw.StringPtr("SCW11111111111111111"),
+					SecretKey:        scw.StringPtr("config-secret"),
+					DefaultProjectID: scw.StringPtr("config-project-id"),
+				},
+			}
+
+			configPath := filepath.Join(ctx.OverrideEnv["HOME"], ".config", "scw", "config.yaml")
+			if err := cfg.SaveTo(configPath); err != nil {
+				return err
+			}
+
+			t.Setenv("SCW_ACCESS_KEY", "SCW99999999999999999")
+			t.Setenv("SCW_SECRET_KEY", "env-secret")
+			t.Setenv("SCW_DEFAULT_PROJECT_ID", "config-project-id")
+
+			return nil
+		},
+		Cmd: "scw test",
+		Check: core.TestCheckCombine(
+			core.TestCheckExitCode(0),
+			func(t *testing.T, ctx *core.CheckFuncCtx) {
+				t.Helper()
+				expected := "" +
+					"Checking multiple variable sources: \n" +
+					"- Variable 'AccessKey' is defined in both config.yaml and environment with different values. " +
+					"Using: environment variable.\n" +
+					"- Variable 'SecretKey' is defined in both config.yaml and environment with different values. " +
+					"Using: environment variable.\n\n"
+
+				assert.Equal(t, expected, ctx.LogBuffer)
+			},
+		),
+	}))
+}
diff --git a/core/testdata/test-check-if-multiple-variable-sources-conflicting-sources-should-trigger-warning.cassette.yaml b/core/testdata/test-check-if-multiple-variable-sources-conflicting-sources-should-trigger-warning.cassette.yaml
new file mode 100644
index 0000000000..4a710de37c
--- /dev/null
+++ b/core/testdata/test-check-if-multiple-variable-sources-conflicting-sources-should-trigger-warning.cassette.yaml
@@ -0,0 +1,35 @@
+---
+version: 1
+interactions:
+- request:
+    body: '{"message":"authentication is denied","method":"api_key","reason":"not_found","type":"denied_authentication"}'
+    form: {}
+    headers:
+      User-Agent:
+      - scaleway-sdk-go/v1.0.0-beta.7+dev (go1.24.4; darwin; arm64) cli-e2e-test
+    url: https://api.scaleway.com/iam/v1alpha1/api-keys/SCWXXXXXXXXXXXXXXXXX
+    method: GET
+  response:
+    body: '{"message":"authentication is denied","method":"api_key","reason":"not_found","type":"denied_authentication"}'
+    headers:
+      Content-Length:
+      - "109"
+      Content-Security-Policy:
+      - default-src 'none'; frame-ancestors 'none'
+      Content-Type:
+      - application/json
+      Date:
+      - Tue, 22 Jul 2025 12:16:22 GMT
+      Server:
+      - Scaleway API Gateway (fr-par-1;edge01)
+      Strict-Transport-Security:
+      - max-age=63072000
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - DENY
+      X-Request-Id:
+      - d55dda1c-064c-4670-95ff-50d7c32fe521
+    status: 401 Unauthorized
+    code: 401
+    duration: ""