diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7cfa586fb86..be050f42596 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -45,6 +45,7 @@
 
 ### Mimirtool
 
+* [ENHANCEMENT] mimirtool analyze: Store the query errors instead of exit during the analysis. #3052
 * [BUGFIX] mimir-tool remote-read: fix returns where some conditions [return nil error even if there is error](https://github.com/grafana/cortex-tools/issues/260). #3053
 
 ### Query-tee
diff --git a/pkg/mimirtool/analyze/prometheus.go b/pkg/mimirtool/analyze/prometheus.go
index 68d4f4a5fba..80b617cc6ea 100644
--- a/pkg/mimirtool/analyze/prometheus.go
+++ b/pkg/mimirtool/analyze/prometheus.go
@@ -12,6 +12,8 @@ type MetricsInPrometheus struct {
 
 	InUseMetricCounts      []MetricCount `json:"in_use_metric_counts"`
 	AdditionalMetricCounts []MetricCount `json:"additional_metric_counts"`
+
+	Errors []string `json:"errors"`
 }
 
 type MetricCount struct {
diff --git a/pkg/mimirtool/commands/analyse_prometheus.go b/pkg/mimirtool/commands/analyse_prometheus.go
index b4c48f4ec9d..b217b91473b 100644
--- a/pkg/mimirtool/commands/analyse_prometheus.go
+++ b/pkg/mimirtool/commands/analyse_prometheus.go
@@ -8,6 +8,7 @@ package commands
 import (
 	"context"
 	"encoding/json"
+	"fmt"
 	"os"
 	"sort"
 	"time"
@@ -98,7 +99,7 @@ func (cmd *PrometheusAnalyzeCommand) run(k *kingpin.ParseContext) error {
 		jobCount   map[string]int
 	}{}
 	inUseCardinality := 0
-
+	var errorMetrics []string
 	for _, metric := range metricsUsed {
 		ctx, cancel := context.WithTimeout(context.Background(), cmd.readTimeout)
 		defer cancel()
@@ -106,7 +107,10 @@ func (cmd *PrometheusAnalyzeCommand) run(k *kingpin.ParseContext) error {
 		query := "count by (job) (" + metric + ")"
 		result, _, err := v1api.Query(ctx, query, time.Now())
 		if err != nil {
-			return errors.Wrap(err, "error querying "+query)
+			errStr := fmt.Sprintf("skipped %s analysis because failed to run query %v: %s", metric, query, err.Error())
+			log.Warnln(errStr)
+			errorMetrics = append(errorMetrics, errStr)
+			continue
 		}
 
 		vec := result.(model.Vector)
@@ -155,7 +159,10 @@ func (cmd *PrometheusAnalyzeCommand) run(k *kingpin.ParseContext) error {
 		query := "count by (job) (" + metric + ")"
 		result, _, err := v1api.Query(ctx, query, time.Now())
 		if err != nil {
-			return errors.Wrap(err, "error querying "+query)
+			errStr := fmt.Sprintf("skipped %s analysis because failed to run query %v: %s", metric, query, err.Error())
+			log.Warnln(errStr)
+			errorMetrics = append(errorMetrics, errStr)
+			continue
 		}
 
 		vec := result.(model.Vector)
@@ -191,6 +198,7 @@ func (cmd *PrometheusAnalyzeCommand) run(k *kingpin.ParseContext) error {
 	output.TotalActiveSeries = inUseCardinality + additionalMetricsCardinality
 	output.InUseActiveSeries = inUseCardinality
 	output.AdditionalActiveSeries = additionalMetricsCardinality
+	output.Errors = errorMetrics
 
 	for metric, counts := range inUseMetrics {
 		jobCounts := make([]analyze.JobCount, 0, len(counts.jobCount))