diff --git a/.changelog/4405.txt b/.changelog/4405.txt
new file mode 100644
index 0000000000..071903d1ab
--- /dev/null
+++ b/.changelog/4405.txt
@@ -0,0 +1,3 @@
+```release-note:bug
+resource/mongodbatlas_advanced_cluster: Emits a warning during plan when `use_effective_fields` is true, auto-scaling is enabled, and `instance_size`, `disk_size_gb`, or `disk_iops` is modified, as Atlas silently ignores these changes in that combination
+```
diff --git a/internal/service/advancedcluster/plan_modifier.go b/internal/service/advancedcluster/plan_modifier.go
index b7431d842a..3477b699d5 100644
--- a/internal/service/advancedcluster/plan_modifier.go
+++ b/internal/service/advancedcluster/plan_modifier.go
@@ -2,6 +2,8 @@ package advancedcluster
 
 import (
 	"context"
+	"fmt"
+	"strings"
 
 	"github.com/hashicorp/terraform-plugin-framework/attr"
 	"github.com/hashicorp/terraform-plugin-framework/diag"
@@ -12,6 +14,9 @@ import (
 )
 
 var (
+	// Spec fields that Atlas controls when auto-scaling is active.
+	autoScalingManagedSpecFields = []string{"instance_size", "disk_size_gb", "disk_iops"}
+
 	// Change mappings uses `attribute_name`, it doesn't care about the nested level.
 	attributeRootChangeMapping = map[string][]string{
 		"replication_specs":      {},
@@ -56,10 +61,37 @@ func handleModifyPlan(ctx context.Context, diags *diag.Diagnostics, state, plan
 	attributeChanges := schemafunc.NewAttributeChanges(ctx, state, plan)
 	keepUnknown := []string{"connection_strings", "state_name", "mongo_db_version", "config_server_type"} // Volatile attributes, should not be copied from state
 	keepUnknown = append(keepUnknown, attributeChanges.KeepUnknown(attributeRootChangeMapping)...)
-	keepUnknown = append(keepUnknown, determineKeepUnknownsAutoScaling(ctx, diags, state, plan)...)
+	autoScalingFields := determineKeepUnknownsAutoScaling(ctx, diags, state, plan)
+	keepUnknown = append(keepUnknown, autoScalingFields...)
+	emitWarningIfSpecChangedWithAutoScaling(ctx, diags, plan, attributeChanges)
 	schemafunc.CopyUnknowns(ctx, state, plan, keepUnknown, nil)
 }
 
+// emitWarningIfSpecChangedWithAutoScaling warns when use_effective_fields=true and auto-scaling is enabled but the user
+// changed instance_size, disk_size_gb, or disk_iops. Atlas silently ignores these changes in that combination
+func emitWarningIfSpecChangedWithAutoScaling(ctx context.Context, diags *diag.Diagnostics, plan *TFModel, attributeChanges schemafunc.AttributeChanges) {
+	if !plan.UseEffectiveFields.ValueBool() || !autoScalingUsed(ctx, diags, plan) {
+		return
+	}
+	var changedFields []string
+	for _, field := range autoScalingManagedSpecFields {
+		if attributeChanges.AttributeChanged(field) {
+			changedFields = append(changedFields, field)
+		}
+	}
+	if len(changedFields) == 0 {
+		return
+	}
+	diags.AddWarning(
+		"Spec change ignored due to auto-scaling",
+		fmt.Sprintf("The change to %s will be stored in Terraform state but will not modify the actual cluster in Atlas. "+
+			"When use_effective_fields is true and auto-scaling is enabled, Atlas controls instance_size, disk_size_gb, and disk_iops values. "+
+			"To apply this change, temporarily disable auto-scaling. "+
+			"See: https://registry.terraform.io/providers/mongodb/mongodbatlas/latest/docs/resources/advanced_cluster#manually-updating-specs-with-use_effective_fields",
+			strings.Join(changedFields, ", ")),
+	)
+}
+
 // adjustRegionConfigsChildren modifies the planned values of region configs based on the current state.
 // This ensures proper handling of removing auto scaling and specs attributes by preserving state values.
 func adjustRegionConfigsChildren(ctx context.Context, diags *diag.Diagnostics, state, plan *TFModel) {
@@ -164,28 +196,26 @@ func findDefinedElectableSpecInReplicationSpec(ctx context.Context, regionConfig
 }
 
 func determineKeepUnknownsAutoScaling(ctx context.Context, diags *diag.Diagnostics, state, plan *TFModel) []string {
-	if !autoScalingUsed(ctx, diags, state, plan) {
+	if !autoScalingUsed(ctx, diags, state) && !autoScalingUsed(ctx, diags, plan) {
 		return nil
 	}
 	// When either compute or disk auto-scaling is enabled, all three fields may be adjusted by Atlas
-	return []string{"instance_size", "disk_size_gb", "disk_iops"}
+	return autoScalingManagedSpecFields
 }
 
-// autoScalingUsed checks if auto-scaling was enabled (state) or will be enabled (plan).
-func autoScalingUsed(ctx context.Context, diags *diag.Diagnostics, state, plan *TFModel) bool {
-	for _, model := range []*TFModel{state, plan} {
-		repSpecsTF := TFModelList[TFReplicationSpecsModel](ctx, diags, model.ReplicationSpecs)
-		for i := range repSpecsTF {
-			regiongConfigsTF := TFModelList[TFRegionConfigsModel](ctx, diags, repSpecsTF[i].RegionConfigs)
-			for j := range regiongConfigsTF {
-				for _, autoScalingTF := range []types.Object{regiongConfigsTF[j].AutoScaling, regiongConfigsTF[j].AnalyticsAutoScaling} {
-					autoscaling := TFModelObject[TFAutoScalingModel](ctx, autoScalingTF)
-					if autoscaling == nil {
-						continue
-					}
-					if autoscaling.ComputeEnabled.ValueBool() || autoscaling.DiskGBEnabled.ValueBool() {
-						return true
-					}
+// autoScalingUsed checks if auto-scaling is enabled in the given cluster model.
+func autoScalingUsed(ctx context.Context, diags *diag.Diagnostics, model *TFModel) bool {
+	repSpecsTF := TFModelList[TFReplicationSpecsModel](ctx, diags, model.ReplicationSpecs)
+	for i := range repSpecsTF {
+		regiongConfigsTF := TFModelList[TFRegionConfigsModel](ctx, diags, repSpecsTF[i].RegionConfigs)
+		for j := range regiongConfigsTF {
+			for _, autoScalingTF := range []types.Object{regiongConfigsTF[j].AutoScaling, regiongConfigsTF[j].AnalyticsAutoScaling} {
+				autoscaling := TFModelObject[TFAutoScalingModel](ctx, autoScalingTF)
+				if autoscaling == nil {
+					continue
+				}
+				if autoscaling.ComputeEnabled.ValueBool() || autoscaling.DiskGBEnabled.ValueBool() {
+					return true
 				}
 			}
 		}