diff --git a/CHANGELOG.md b/CHANGELOG.md
index adfa54b03e..a12bcd6616 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,7 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 ### Fixed
 
 * [#7511](https://github.com/thanos-io/thanos/pull/7511) Query Frontend: fix doubled gzip compression for response body.
+* [#7592](https://github.com/thanos-io/thanos/pull/7592) Ruler: Only increment `thanos_rule_evaluation_with_warnings_total` metric for non PromQL warnings.
 
 ### Added
 
diff --git a/cmd/thanos/rule.go b/cmd/thanos/rule.go
index 09c928fb6e..6c8fbea6e9 100644
--- a/cmd/thanos/rule.go
+++ b/cmd/thanos/rule.go
@@ -40,12 +40,12 @@ import (
 	"github.com/prometheus/prometheus/tsdb"
 	"github.com/prometheus/prometheus/tsdb/agent"
 	"github.com/prometheus/prometheus/tsdb/wlog"
+	"gopkg.in/yaml.v2"
 
 	"github.com/thanos-io/objstore"
 	"github.com/thanos-io/objstore/client"
 	objstoretracing "github.com/thanos-io/objstore/tracing/opentracing"
 	"github.com/thanos-io/promql-engine/execution/parse"
-	"gopkg.in/yaml.v2"
 
 	"github.com/thanos-io/thanos/pkg/alert"
 	v1 "github.com/thanos-io/thanos/pkg/api/rule"
@@ -54,6 +54,7 @@ import (
 	"github.com/thanos-io/thanos/pkg/component"
 	"github.com/thanos-io/thanos/pkg/discovery/dns"
 	"github.com/thanos-io/thanos/pkg/errutil"
+	"github.com/thanos-io/thanos/pkg/extannotations"
 	"github.com/thanos-io/thanos/pkg/extgrpc"
 	"github.com/thanos-io/thanos/pkg/extkingpin"
 	"github.com/thanos-io/thanos/pkg/extprom"
@@ -292,7 +293,7 @@ func newRuleMetrics(reg *prometheus.Registry) *RuleMetrics {
 	m.ruleEvalWarnings = factory.NewCounterVec(
 		prometheus.CounterOpts{
 			Name: "thanos_rule_evaluation_with_warnings_total",
-			Help: "The total number of rule evaluation that were successful but had warnings which can indicate partial error.",
+			Help: "The total number of rule evaluation that were successful but had non PromQL warnings which can indicate partial error.",
 		}, []string{"strategy"},
 	)
 	m.ruleEvalWarnings.WithLabelValues(strings.ToLower(storepb.PartialResponseStrategy_ABORT.String()))
@@ -939,6 +940,8 @@ func queryFuncCreator(
 						level.Error(logger).Log("err", err, "query", qs)
 						continue
 					}
+
+					warns = filterOutPromQLWarnings(warns, logger, qs)
 					if len(warns) > 0 {
 						ruleEvalWarnings.WithLabelValues(strings.ToLower(partialResponseStrategy.String())).Inc()
 						// TODO(bwplotka): Propagate those to UI, probably requires changing rule manager code ):
@@ -970,12 +973,13 @@ func queryFuncCreator(
 						continue
 					}
 
-					if len(result.Warnings) > 0 {
+					warnings := make([]string, 0, len(result.Warnings))
+					for _, warn := range result.Warnings {
+						warnings = append(warnings, warn.Error())
+					}
+					warnings = filterOutPromQLWarnings(warnings, logger, qs)
+					if len(warnings) > 0 {
 						ruleEvalWarnings.WithLabelValues(strings.ToLower(partialResponseStrategy.String())).Inc()
-						warnings := make([]string, 0, len(result.Warnings))
-						for _, w := range result.Warnings {
-							warnings = append(warnings, w.Error())
-						}
 						level.Warn(logger).Log("warnings", strings.Join(warnings, ", "), "query", qs)
 					}
 
@@ -1081,3 +1085,16 @@ func validateTemplate(tmplStr string) error {
 	}
 	return nil
 }
+
+// Filter out PromQL related warnings from warning response and keep store related warnings only.
+func filterOutPromQLWarnings(warns []string, logger log.Logger, query string) []string {
+	storeWarnings := make([]string, 0, len(warns))
+	for _, warn := range warns {
+		if extannotations.IsPromQLAnnotation(warn) {
+			level.Warn(logger).Log("warning", warn, "query", query)
+			continue
+		}
+		storeWarnings = append(storeWarnings, warn)
+	}
+	return storeWarnings
+}
diff --git a/cmd/thanos/rule_test.go b/cmd/thanos/rule_test.go
index 097b66e65b..28d1421fa8 100644
--- a/cmd/thanos/rule_test.go
+++ b/cmd/thanos/rule_test.go
@@ -7,6 +7,10 @@ import (
 	"testing"
 
 	"github.com/efficientgo/core/testutil"
+	"github.com/go-kit/log"
+	"github.com/prometheus/prometheus/util/annotations"
+
+	"github.com/thanos-io/thanos/pkg/extpromql"
 )
 
 func Test_parseFlagLabels(t *testing.T) {
@@ -110,3 +114,59 @@ func Test_tableLinkForExpression(t *testing.T) {
 		testutil.Equals(t, resStr, td.expectStr)
 	}
 }
+
+func TestFilterOutPromQLWarnings(t *testing.T) {
+	logger := log.NewNopLogger()
+	query := "foo"
+	expr, err := extpromql.ParseExpr(`rate(prometheus_build_info[5m])`)
+	testutil.Ok(t, err)
+	possibleCounterInfo := annotations.NewPossibleNonCounterInfo("foo", expr.PositionRange())
+	badBucketLabelWarning := annotations.NewBadBucketLabelWarning("foo", "0.99", expr.PositionRange())
+	for _, tc := range []struct {
+		name     string
+		warnings []string
+		expected []string
+	}{
+		{
+			name:     "nil warning",
+			expected: make([]string, 0),
+		},
+		{
+			name:     "empty warning",
+			warnings: make([]string, 0),
+			expected: make([]string, 0),
+		},
+		{
+			name: "no PromQL warning",
+			warnings: []string{
+				"some_warning_message",
+			},
+			expected: []string{
+				"some_warning_message",
+			},
+		},
+		{
+			name: "PromQL warning",
+			warnings: []string{
+				possibleCounterInfo.Error(),
+			},
+			expected: make([]string, 0),
+		},
+		{
+			name: "filter out all PromQL warnings",
+			warnings: []string{
+				possibleCounterInfo.Error(),
+				badBucketLabelWarning.Error(),
+				"some_warning_message",
+			},
+			expected: []string{
+				"some_warning_message",
+			},
+		},
+	} {
+		t.Run(tc.name, func(t *testing.T) {
+			output := filterOutPromQLWarnings(tc.warnings, logger, query)
+			testutil.Equals(t, tc.expected, output)
+		})
+	}
+}