diff --git a/promql/functions.go b/promql/functions.go
index 35dbd2970..018023bf0 100644
--- a/promql/functions.go
+++ b/promql/functions.go
@@ -179,15 +179,21 @@ func extrapolatedRate(vals []parser.Value, args parser.Expressions, enh *EvalNod
 // Otherwise, it returns the calculated histogram and an empty annotation.
 func histogramRate(points []HPoint, isCounter bool, metricName string, pos posrange.PositionRange) (*histogram.FloatHistogram, annotations.Annotations) {
 	prev := points[0].H
+	usingCustomBuckets := prev.UsesCustomBuckets()
 	last := points[len(points)-1].H
 	if last == nil {
 		return nil, annotations.New().Add(annotations.NewMixedFloatsHistogramsWarning(metricName, pos))
 	}
+
 	minSchema := prev.Schema
 	if last.Schema < minSchema {
 		minSchema = last.Schema
 	}
 
+	if last.UsesCustomBuckets() != usingCustomBuckets {
+		return nil, annotations.New().Add(annotations.NewMixedExponentialCustomHistogramsWarning(metricName, pos))
+	}
+
 	var annos annotations.Annotations
 
 	// We check for gauge type histograms in the loop below, but the loop below does not run on the first and last point,
@@ -215,6 +221,9 @@ func histogramRate(points []HPoint, isCounter bool, metricName string, pos posra
 		if curr.Schema < minSchema {
 			minSchema = curr.Schema
 		}
+		if curr.UsesCustomBuckets() != usingCustomBuckets {
+			return nil, annotations.New().Add(annotations.NewMixedExponentialCustomHistogramsWarning(metricName, pos))
+		}
 	}
 
 	h := last.CopyToSchema(minSchema)
diff --git a/promql/promqltest/test.go b/promql/promqltest/test.go
index 83137e661..8b1ec381a 100644
--- a/promql/promqltest/test.go
+++ b/promql/promqltest/test.go
@@ -1003,13 +1003,6 @@ func (t *test) execRangeEval(cmd *evalCmd, engine promql.QueryEngine) error {
 		return fmt.Errorf("error creating range query for %q (line %d): %w", cmd.expr, cmd.line, err)
 	}
 	res := q.Exec(t.context)
-	countWarnings, _ := res.Warnings.CountWarningsAndInfo()
-	if !cmd.warn && countWarnings > 0 {
-		return fmt.Errorf("unexpected warnings evaluating query %q (line %d): %v", cmd.expr, cmd.line, res.Warnings)
-	}
-	if cmd.warn && countWarnings == 0 {
-		return fmt.Errorf("expected warnings evaluating query %q (line %d) but got none", cmd.expr, cmd.line)
-	}
 	if res.Err != nil {
 		if cmd.fail {
 			return cmd.checkExpectedFailure(res.Err)
@@ -1020,6 +1013,13 @@ func (t *test) execRangeEval(cmd *evalCmd, engine promql.QueryEngine) error {
 	if res.Err == nil && cmd.fail {
 		return fmt.Errorf("expected error evaluating query %q (line %d) but got none", cmd.expr, cmd.line)
 	}
+	countWarnings, _ := res.Warnings.CountWarningsAndInfo()
+	if !cmd.warn && countWarnings > 0 {
+		return fmt.Errorf("unexpected warnings evaluating query %q (line %d): %v", cmd.expr, cmd.line, res.Warnings)
+	}
+	if cmd.warn && countWarnings == 0 {
+		return fmt.Errorf("expected warnings evaluating query %q (line %d) but got none", cmd.expr, cmd.line)
+	}
 	defer q.Close()
 
 	if err := cmd.compareResult(res.Value); err != nil {
@@ -1050,13 +1050,6 @@ func (t *test) runInstantQuery(iq atModifierTestCase, cmd *evalCmd, engine promq
 	}
 	defer q.Close()
 	res := q.Exec(t.context)
-	countWarnings, _ := res.Warnings.CountWarningsAndInfo()
-	if !cmd.warn && countWarnings > 0 {
-		return fmt.Errorf("unexpected warnings evaluating query %q (line %d): %v", iq.expr, cmd.line, res.Warnings)
-	}
-	if cmd.warn && countWarnings == 0 {
-		return fmt.Errorf("expected warnings evaluating query %q (line %d) but got none", iq.expr, cmd.line)
-	}
 	if res.Err != nil {
 		if cmd.fail {
 			if err := cmd.checkExpectedFailure(res.Err); err != nil {
@@ -1070,6 +1063,13 @@ func (t *test) runInstantQuery(iq atModifierTestCase, cmd *evalCmd, engine promq
 	if res.Err == nil && cmd.fail {
 		return fmt.Errorf("expected error evaluating query %q (line %d) but got none", iq.expr, cmd.line)
 	}
+	countWarnings, _ := res.Warnings.CountWarningsAndInfo()
+	if !cmd.warn && countWarnings > 0 {
+		return fmt.Errorf("unexpected warnings evaluating query %q (line %d): %v", iq.expr, cmd.line, res.Warnings)
+	}
+	if cmd.warn && countWarnings == 0 {
+		return fmt.Errorf("expected warnings evaluating query %q (line %d) but got none", iq.expr, cmd.line)
+	}
 	err = cmd.compareResult(res.Value)
 	if err != nil {
 		return fmt.Errorf("error in %s %s (line %d): %w", cmd, iq.expr, cmd.line, err)
diff --git a/promql/promqltest/testdata/native_histograms.test b/promql/promqltest/testdata/native_histograms.test
index 034d73eb5..f91626c34 100644
--- a/promql/promqltest/testdata/native_histograms.test
+++ b/promql/promqltest/testdata/native_histograms.test
@@ -762,3 +762,25 @@ eval_warn instant at 30s rate(some_metric[30s])
 # Test the case where we have more than two points for rate
 eval_warn instant at 1m rate(some_metric[1m])
     {} {{count:0.03333333333333333 sum:0.03333333333333333 buckets:[0.03333333333333333]}}
+
+clear
+
+# Test rate() over mixed exponential and custom buckets.
+load 30s
+    some_metric {{schema:0 sum:1 count:1 buckets:[1]}} {{schema:-53 sum:1 count:1 custom_values:[5 10] buckets:[1]}} {{schema:0 sum:5 count:4 buckets:[1 2 1]}} {{schema:-53 sum:1 count:1 custom_values:[5 10] buckets:[1]}}
+
+# Start and end with exponential, with custom in the middle.
+eval_warn instant at 1m rate(some_metric[1m])
+    # Should produce no results.
+
+# Start and end with custom, with exponential in the middle.
+eval_warn instant at 1m30s rate(some_metric[1m])
+    # Should produce no results.
+
+# Start with custom, end with exponential.
+eval_warn instant at 1m rate(some_metric[30s])
+    # Should produce no results.
+
+# Start with exponential, end with custom.
+eval_warn instant at 30s rate(some_metric[30s])
+    # Should produce no results.