diff --git a/go.mod b/go.mod
index e4950635a..afc88a77b 100644
--- a/go.mod
+++ b/go.mod
@@ -11,6 +11,7 @@ require (
 	github.com/go-kit/log v0.2.1
 	github.com/google/go-cmp v0.7.0
 	github.com/google/go-github/v29 v29.0.3
+	github.com/google/shlex v0.0.0-20191202100458-e7afc7fbc510
 	github.com/nelkinda/health-go v0.0.1
 	github.com/oklog/run v1.2.0
 	github.com/prometheus/alertmanager v0.31.1
diff --git a/pkg/provider/provider.go b/pkg/provider/provider.go
index 92e764a53..d244ed4ba 100644
--- a/pkg/provider/provider.go
+++ b/pkg/provider/provider.go
@@ -127,17 +127,37 @@ func RetryUntilTrue(name string, retryCount int, fn func() (bool, error)) error
 	return fmt.Errorf("Request for '%v' hasn't completed after retrying %d times", name, retryCount)
 }
 
+// prometheusArgs builds a YAML flow-sequence injection string starting with
+// baseArg, followed by any space-separated flags from extraFlags. The returned
+// value is intended to be placed inside a double-quoted YAML string: the
+// embedded "," separators will break into additional flow-sequence items after
+// template rendering, e.g. "--log.level=info","--flag1","--flag2".
+func prometheusArgs(baseArg, extraFlags string) string {
+	parts := []string{baseArg}
+	for _, f := range strings.Fields(extraFlags) {
+		parts = append(parts, strings.ReplaceAll(f, `"`, `\"`))
+	}
+	return strings.Join(parts, `","`)
+}
+
 // applyTemplateVars applies golang templates to deployment files.
 func applyTemplateVars(content []byte, deploymentVars map[string]string) ([]byte, error) {
 	fileContentParsed := bytes.NewBufferString("")
 	t := template.New("resource").Option("missingkey=error")
 	t = t.Funcs(template.FuncMap{
-		// k8s objects can't have dots(.) se we add a custom function to allow normalising the variable values.
+		// k8s objects can't have dots(.) so we add a custom function to allow normalising the variable values.
 		"normalise": func(t string) string {
 			return strings.ReplaceAll(t, ".", "-")
 		},
-		"split": func(rangeVars, separator string) []string {
-			return strings.Split(rangeVars, separator)
+		// prArgs returns a YAML flow-sequence injection string for the PR prometheus
+		// instance, including --log.level=info and any PR_EXTRA_FLAGS.
+		"prArgs": func(vars map[string]string) string {
+			return prometheusArgs("--log.level=info", vars["PR_EXTRA_FLAGS"])
+		},
+		// mainArgs returns a YAML flow-sequence injection string for the main/release
+		// prometheus instance, including --log.level=info and any MAIN_EXTRA_FLAGS.
+		"mainArgs": func(vars map[string]string) string {
+			return prometheusArgs("--log.level=info", vars["MAIN_EXTRA_FLAGS"])
 		},
 	})
 	if err := template.Must(t.Parse(string(content))).Execute(fileContentParsed, deploymentVars); err != nil {
diff --git a/prombench/Makefile b/prombench/Makefile
index b3a537146..e88b507ed 100644
--- a/prombench/Makefile
+++ b/prombench/Makefile
@@ -95,6 +95,8 @@ resource_apply:
 		-v CLUSTER_NAME:${CLUSTER_NAME} \
 		-v PR_NUMBER:${PR_NUMBER} -v RELEASE:${RELEASE} -v DOMAIN_NAME:${DOMAIN_NAME} \
 		-v GITHUB_ORG:${GITHUB_ORG} -v GITHUB_REPO:${GITHUB_REPO} \
+		$(if $(PR_EXTRA_FLAGS),-v "PR_EXTRA_FLAGS:$(PR_EXTRA_FLAGS)") \
+		$(if $(MAIN_EXTRA_FLAGS),-v "MAIN_EXTRA_FLAGS:$(MAIN_EXTRA_FLAGS)") \
 		-f ${PROMBENCH_DIR}/${BENCHMARK_DIRECTORY}/benchmark
 
 # Required because namespace and cluster-role are not part of the created nodes
diff --git a/prombench/manifests/cluster-infra/7a_commentmonitor_configmap_noparse.yaml b/prombench/manifests/cluster-infra/7a_commentmonitor_configmap_noparse.yaml
index 53a59fc35..e59c0d813 100644
--- a/prombench/manifests/cluster-infra/7a_commentmonitor_configmap_noparse.yaml
+++ b/prombench/manifests/cluster-infra/7a_commentmonitor_configmap_noparse.yaml
@@ -18,6 +18,8 @@ data:
           * See the details [here](https://github.com/prometheus/test-infra/tree/master/prombench/manifests/prombench#benchmarking-from-the-different-directory), defaults to `manifests/prombench`.
         * `--bench.version=<branch | @commit>`
           * See the details [here](https://github.com/prometheus/test-infra/tree/master/prombench/manifests/prombench#benchmarking-from-the-custom-test-infra-commitbranch), defaults to `master`.
+        * `--pr.extra-flags=<space-separated Prometheus flags>` - extra flags passed to the PR Prometheus instance.
+        * `--main.extra-flags=<space-separated Prometheus flags>` - extra flags passed to the main/release Prometheus instance.
 
         **Examples:**
         * `/prombench v3.0.0`
@@ -37,6 +39,8 @@ data:
         flag_args:
           bench.directory: BENCHMARK_DIRECTORY
           bench.version: BENCHMARK_VERSION
+          pr.extra-flags: PR_EXTRA_FLAGS
+          main.extra-flags: MAIN_EXTRA_FLAGS
         comment_template: |
           ⏱️ Welcome (again) to Prometheus Benchmarking Tool. ⏱️
 
@@ -59,7 +63,7 @@ data:
           - [Parca profiles (e.g. in-use memory)](http://{{ index . "DOMAIN_NAME" }}/profiles?expression_a=memory%3Ainuse_space%3Abytes%3Aspace%3Abytes%7Bpr_number%3D%22{{ index . "PR_NUMBER" }}%22%7D&time_selection_a=relative:minute|15)
 
           **Available Commands:**
-          * To restart benchmark: `/prombench restart {{ index . "RELEASE" }}{{ if index . "BENCHMARK_VERSION" }} --bench.version={{ index . "BENCHMARK_VERSION" }}{{ end }}{{ if index . "BENCHMARK_DIRECTORY" }} --bench.directory={{ index . "BENCHMARK_DIRECTORY" }}{{ end }}`
+          * To restart benchmark: `/prombench restart {{ index . "RELEASE" }}{{ if index . "BENCHMARK_VERSION" }} --bench.version={{ index . "BENCHMARK_VERSION" }}{{ end }}{{ if index . "BENCHMARK_DIRECTORY" }} --bench.directory={{ index . "BENCHMARK_DIRECTORY" }}{{ end }}{{ if index . "PR_EXTRA_FLAGS" }} --pr.extra-flags={{ index . "PR_EXTRA_FLAGS" }}{{ end }}{{ if index . "MAIN_EXTRA_FLAGS" }} --main.extra-flags={{ index . "MAIN_EXTRA_FLAGS" }}{{ end }}`
           * To stop benchmark: `/prombench cancel`
           * To print help: `/prombench help`
 
@@ -70,6 +74,8 @@ data:
         flag_args:
           bench.directory: BENCHMARK_DIRECTORY
           bench.version: BENCHMARK_VERSION
+          pr.extra-flags: PR_EXTRA_FLAGS
+          main.extra-flags: MAIN_EXTRA_FLAGS
         label: prombench
         comment_template: |
           ⏱️ Welcome to Prometheus Benchmarking Tool. ⏱️
@@ -93,6 +99,6 @@ data:
           - [Parca profiles (e.g. in-use memory)](http://{{ index . "DOMAIN_NAME" }}/profiles?expression_a=memory%3Ainuse_space%3Abytes%3Aspace%3Abytes%7Bpr_number%3D%22{{ index . "PR_NUMBER" }}%22%7D&time_selection_a=relative:minute|15)
 
           **Available Commands:**
-          * To restart benchmark: `/prombench restart {{ index . "RELEASE" }}{{ if index . "BENCHMARK_VERSION" }} --bench.version={{ index . "BENCHMARK_VERSION" }}{{ end }}{{ if index . "BENCHMARK_DIRECTORY" }} --bench.directory={{ index . "BENCHMARK_DIRECTORY" }}{{ end }}`
+          * To restart benchmark: `/prombench restart {{ index . "RELEASE" }}{{ if index . "BENCHMARK_VERSION" }} --bench.version={{ index . "BENCHMARK_VERSION" }}{{ end }}{{ if index . "BENCHMARK_DIRECTORY" }} --bench.directory={{ index . "BENCHMARK_DIRECTORY" }}{{ end }}{{ if index . "PR_EXTRA_FLAGS" }} --pr.extra-flags={{ index . "PR_EXTRA_FLAGS" }}{{ end }}{{ if index . "MAIN_EXTRA_FLAGS" }} --main.extra-flags={{ index . "MAIN_EXTRA_FLAGS" }}{{ end }}`
           * To stop benchmark: `/prombench cancel`
           * To print help: `/prombench help`
diff --git a/prombench/manifests/prombench/benchmark/5_prometheus-test-pr_deployment.yaml b/prombench/manifests/prombench/benchmark/5_prometheus-test-pr_deployment.yaml
index 4278bee38..2fd02a175 100644
--- a/prombench/manifests/prombench/benchmark/5_prometheus-test-pr_deployment.yaml
+++ b/prombench/manifests/prombench/benchmark/5_prometheus-test-pr_deployment.yaml
@@ -814,7 +814,7 @@ spec:
           "--web.external-url=http://{{ .DOMAIN_NAME }}/{{ .PR_NUMBER }}/prometheus-pr",
           "--storage.tsdb.path=/prometheus",
           "--config.file=/etc/prometheus/prometheus.yml",
-          "--log.level=info"
+          "{{prArgs .}}"
         ]
         resources:
           requests:
diff --git a/prombench/manifests/prombench/benchmark/5_prometheus-test-release_deployment.yaml b/prombench/manifests/prombench/benchmark/5_prometheus-test-release_deployment.yaml
index dda0cd38d..ea98d5353 100644
--- a/prombench/manifests/prombench/benchmark/5_prometheus-test-release_deployment.yaml
+++ b/prombench/manifests/prombench/benchmark/5_prometheus-test-release_deployment.yaml
@@ -789,7 +789,7 @@ spec:
           "--web.external-url=http://{{ .DOMAIN_NAME }}/{{ .PR_NUMBER }}/prometheus-release",
           "--storage.tsdb.path=/prometheus",
           "--config.file=/etc/prometheus/prometheus.yml",
-          "--log.level=info"
+          "{{mainArgs .}}"
         ]
         resources:
           requests:
diff --git a/tools/comment-monitor/internal/command.go b/tools/comment-monitor/internal/command.go
index 28430aa4a..756c6439f 100644
--- a/tools/comment-monitor/internal/command.go
+++ b/tools/comment-monitor/internal/command.go
@@ -22,6 +22,7 @@ import (
 	"strings"
 	"text/template"
 
+	"github.com/google/shlex"
 	"gopkg.in/yaml.v2"
 )
 
@@ -167,7 +168,13 @@ func ParseCommand(cfg *Config, comment string) (_ *Command, ok bool, err *Comman
 		i = len(comment)
 	}
 	cmdLine := comment[:i]
-	rest := strings.Split(strings.TrimSpace(cmdLine[len(prefix.Prefix):]), " ")
+	rest, tErr := shlex.Split(strings.TrimSpace(cmdLine[len(prefix.Prefix):]))
+	if tErr != nil {
+		return nil, false, &CommandParseError{
+			error: fmt.Errorf("tokenizing command line failed for %v: %w", cmdLine, tErr),
+			help:  fmt.Sprintf("Incorrect `%v` syntax; %v.\n\n%s", prefix.Prefix, tErr.Error(), prefix.Help),
+		}
+	}
 	if len(rest) == 0 || rest[0] == "" {
 		return nil, false, &CommandParseError{
 			error: fmt.Errorf("no matching command found for comment line: %v", cmdLine),
@@ -261,21 +268,20 @@ func ParseCommand(cfg *Config, comment string) (_ *Command, ok bool, err *Comman
 }
 
 func parseFlags(rest []string, cfg *CommandConfig, cmd *Command) error {
-	// TODO(bwplotka: Naive flag parsing, make it support quoting, spaces etc later.
 	for _, flag := range rest {
 		if !strings.HasPrefix(flag, "--") {
 			return fmt.Errorf("expected flag (starting with --), got %v", flag)
 		}
-		parts := strings.Split(flag, "=")
-		if len(parts) != 2 {
+		eqIdx := strings.Index(flag, "=")
+		if eqIdx == -1 {
 			return fmt.Errorf("expected flag format '--<flag>=<value>', got %v", flag)
 		}
 
-		argName, ok := cfg.FlagArgs[strings.TrimPrefix(parts[0], "--")]
+		argName, ok := cfg.FlagArgs[strings.TrimPrefix(flag[:eqIdx], "--")]
 		if !ok {
 			return fmt.Errorf("flag %v is not supported", flag)
 		}
-		cmd.Args[argName] = parts[1]
+		cmd.Args[argName] = flag[eqIdx+1:]
 	}
 	return nil
 }
diff --git a/tools/comment-monitor/internal/command_test.go b/tools/comment-monitor/internal/command_test.go
index a0014b934..00df62e38 100644
--- a/tools/comment-monitor/internal/command_test.go
+++ b/tools/comment-monitor/internal/command_test.go
@@ -146,6 +146,22 @@ func TestParseCommand(t *testing.T) {
 			comment: "/prombench v3.0.0 --bench.version=yolo --bench.directory=dir1",
 			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "BENCHMARK_VERSION": "yolo", "BENCHMARK_DIRECTORY": "dir1"}),
 		},
+		{
+			comment: "/prombench v3.0.0 --pr.extra-flags=--enable-feature=foo",
+			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "PR_EXTRA_FLAGS": "--enable-feature=foo"}),
+		},
+		{
+			comment: "/prombench v3.0.0 --main.extra-flags=--enable-feature=bar",
+			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "MAIN_EXTRA_FLAGS": "--enable-feature=bar"}),
+		},
+		{
+			comment: "/prombench restart v3.0.0 --pr.extra-flags=--enable-feature=foo --main.extra-flags=--enable-feature=bar",
+			expect:  testCommand(eventTypeRestart, map[string]string{"RELEASE": "v3.0.0", "PR_EXTRA_FLAGS": "--enable-feature=foo", "MAIN_EXTRA_FLAGS": "--enable-feature=bar"}),
+		},
+		{
+			comment: "/prombench v3.0.0 --pr.extra-flags='--enable-feature=foo --enable-feature=bar'",
+			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "PR_EXTRA_FLAGS": "--enable-feature=foo --enable-feature=bar"}),
+		},
 		// Text at the end is generally accepted, after \n.
 		{
 			comment: "/prombench v3.0.0\n",
@@ -262,6 +278,22 @@ func TestParseCommand_ProdCommentMonitorConfig(t *testing.T) {
 			comment: "/prombench v3.0.0 --bench.version=mybranch --bench.directory=manifests/prombench",
 			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "BENCHMARK_VERSION": "mybranch", "BENCHMARK_DIRECTORY": "manifests/prombench"}),
 		},
+		{
+			comment: "/prombench v3.0.0 --pr.extra-flags=--enable-feature=foo",
+			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "PR_EXTRA_FLAGS": "--enable-feature=foo"}),
+		},
+		{
+			comment: "/prombench v3.0.0 --main.extra-flags=--enable-feature=bar",
+			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "MAIN_EXTRA_FLAGS": "--enable-feature=bar"}),
+		},
+		{
+			comment: "/prombench restart v3.0.0 --pr.extra-flags=--enable-feature=foo --main.extra-flags=--enable-feature=bar",
+			expect:  testCommand(eventTypeRestart, map[string]string{"RELEASE": "v3.0.0", "PR_EXTRA_FLAGS": "--enable-feature=foo", "MAIN_EXTRA_FLAGS": "--enable-feature=bar"}),
+		},
+		{
+			comment: "/prombench v3.0.0 --pr.extra-flags='--enable-feature=foo --enable-feature=bar'",
+			expect:  testCommand(eventTypeStart, map[string]string{"RELEASE": "v3.0.0", "PR_EXTRA_FLAGS": "--enable-feature=foo --enable-feature=bar"}),
+		},
 		// Not matching cases.
 		{comment: ""},
 		{comment: "How to start prombench? I think it was something like:\n\n /prombench main\n\nYolo"},
diff --git a/tools/comment-monitor/internal/testdata/testconfig.yaml b/tools/comment-monitor/internal/testdata/testconfig.yaml
index 28aca4c62..323504095 100644
--- a/tools/comment-monitor/internal/testdata/testconfig.yaml
+++ b/tools/comment-monitor/internal/testdata/testconfig.yaml
@@ -27,6 +27,8 @@ prefixes:
     flag_args:
       bench.directory: BENCHMARK_DIRECTORY
       bench.version: BENCHMARK_VERSION
+      pr.extra-flags: PR_EXTRA_FLAGS
+      main.extra-flags: MAIN_EXTRA_FLAGS
 
   - name: "" # start is a default (empty command).
     event_type: prombench_start
@@ -35,4 +37,6 @@ prefixes:
     flag_args:
       bench.directory: BENCHMARK_DIRECTORY
       bench.version: BENCHMARK_VERSION
+      pr.extra-flags: PR_EXTRA_FLAGS
+      main.extra-flags: MAIN_EXTRA_FLAGS
     label: prombench