diff --git a/cmd/jaeger/internal/integration/kafka_test.go b/cmd/jaeger/internal/integration/kafka_test.go
index b98eb3d819a..45038e335b6 100644
--- a/cmd/jaeger/internal/integration/kafka_test.go
+++ b/cmd/jaeger/internal/integration/kafka_test.go
@@ -4,46 +4,117 @@
 package integration
 
 import (
+	"fmt"
+	"os"
+	"path/filepath"
 	"testing"
+	"time"
+
+	"github.com/stretchr/testify/require"
+	"gopkg.in/yaml.v3"
 
 	"github.com/jaegertracing/jaeger/plugin/storage/integration"
 )
 
+// createConfigWithEncoding rewrites the base configuration files to use the given encoding
+// and Kafka topic which are varied between the test runs.
+//
+// Once OTEL Collector supports default values for env vars
+// (https://github.com/open-telemetry/opentelemetry-collector/issues/5228)
+// we can change the config to use topic: "${KAFKA_TOPIC:-jaeger-spans}"
+// and export a KAFKA_TOPIC var with random topic name in the tests.
+func createConfigWithEncoding(t *testing.T, configFile string, targetEncoding string, uniqueTopic string) string {
+	data, err := os.ReadFile(configFile)
+	require.NoError(t, err, "Failed to read config file: %s", configFile)
+
+	var config map[string]any
+	err = yaml.Unmarshal(data, &config)
+	require.NoError(t, err, "Failed to unmarshal YAML data from config file: %s", configFile)
+
+	// Function to recursively search and replace the encoding and topic
+	var replaceEncodingAndTopic func(m map[string]any) int
+	replaceEncodingAndTopic = func(m map[string]any) int {
+		replacements := 0
+		for k, v := range m {
+			if k == "encoding" {
+				oldEncoding := v.(string)
+				m[k] = targetEncoding
+				t.Logf("Replaced encoding '%s' with '%s' in key: %s", oldEncoding, targetEncoding, k)
+				replacements++
+			} else if k == "topic" {
+				oldTopic := v.(string)
+				m[k] = uniqueTopic
+				t.Logf("Replaced topic '%s' with '%s' in key: %s", oldTopic, uniqueTopic, k)
+				replacements++
+			} else if subMap, ok := v.(map[string]any); ok {
+				replacements += replaceEncodingAndTopic(subMap)
+			}
+		}
+		return replacements
+	}
+
+	totalReplacements := replaceEncodingAndTopic(config)
+	require.Equal(t, 2, totalReplacements, "Expected exactly 2 replacements (encoding and topic), but got %d", totalReplacements)
+
+	newData, err := yaml.Marshal(config)
+	require.NoError(t, err, "Failed to marshal YAML data after encoding replacement")
+
+	tempFile := filepath.Join(t.TempDir(), fmt.Sprintf("config_%s.yaml", targetEncoding))
+	err = os.WriteFile(tempFile, newData, 0o600)
+	require.NoError(t, err, "Failed to write updated config file to: %s", tempFile)
+
+	t.Logf("Configuration file with encoding '%s' and topic '%s' written to: %s", targetEncoding, uniqueTopic, tempFile)
+
+	return tempFile
+}
+
 func TestKafkaStorage(t *testing.T) {
 	integration.SkipUnlessEnv(t, "kafka")
 
-	// TODO these config files use topic: "jaeger-spans",
-	// but for integration tests we want to use random topic in each run.
-	// https://github.com/jaegertracing/jaeger/blob/ed5cc2981c34158d0650cb96cb2fafcb753bea70/plugin/storage/integration/kafka_test.go#L50-L51
-	// Once OTEL Collector supports default values for env vars
-	// (https://github.com/open-telemetry/opentelemetry-collector/issues/5228)
-	// we can change the config to use topic: "${KAFKA_TOPIC:-jaeger-spans}"
-	// and export a KAFKA_TOPIC var with random topic name in the tests.
-
-	collectorConfig := "../../collector-with-kafka.yaml"
-	ingesterConfig := "../../ingester-remote-storage.yaml"
-
-	collector := &E2EStorageIntegration{
-		SkipStorageCleaner:  true,
-		ConfigFile:          collectorConfig,
-		HealthCheckEndpoint: "http://localhost:8888/metrics",
+	tests := []struct {
+		encoding string
+		skip     string
+	}{
+		{encoding: "otlp_proto"},
+		{encoding: "otlp_json", skip: "not supported: https://github.com/open-telemetry/opentelemetry-collector-contrib/issues/33627"},
+		{encoding: "jaeger_proto"},
+		{encoding: "jaeger_json"},
 	}
 
-	// Initialize and start the collector
-	collector.e2eInitialize(t, "kafka")
+	for _, test := range tests {
+		t.Run(test.encoding, func(t *testing.T) {
+			if test.skip != "" {
+				t.Skip(test.skip)
+			}
+			uniqueTopic := fmt.Sprintf("jaeger-spans-%d", time.Now().UnixNano())
+			t.Logf("Using unique Kafka topic: %s", uniqueTopic)
 
-	ingester := &E2EStorageIntegration{
-		ConfigFile: ingesterConfig,
-		StorageIntegration: integration.StorageIntegration{
-			CleanUp:                      purge,
-			GetDependenciesReturnsSource: true,
-			SkipArchiveTest:              true,
-		},
-	}
+			// Unlike the other storage tests where "collector" has access to the storage,
+			// here we have two distinct binaries, collector and ingester, and only the ingester
+			// has access to the storage and allows the test to query it.
+			// We reuse E2EStorageIntegration struct to manage lifecycle of the collector,
+			// but the tests are run against the ingester.
+
+			collector := &E2EStorageIntegration{
+				SkipStorageCleaner:  true,
+				ConfigFile:          createConfigWithEncoding(t, "../../collector-with-kafka.yaml", test.encoding, uniqueTopic),
+				HealthCheckEndpoint: "http://localhost:8888/metrics",
+			}
+			collector.e2eInitialize(t, "kafka")
+			t.Log("Collector initialized")
 
-	// Initialize and start the ingester
-	ingester.e2eInitialize(t, "kafka")
+			ingester := &E2EStorageIntegration{
+				ConfigFile: createConfigWithEncoding(t, "../../ingester-remote-storage.yaml", test.encoding, uniqueTopic),
+				StorageIntegration: integration.StorageIntegration{
+					CleanUp:                      purge,
+					GetDependenciesReturnsSource: true,
+					SkipArchiveTest:              true,
+				},
+			}
+			ingester.e2eInitialize(t, "kafka")
+			t.Log("Ingester initialized")
 
-	// Run the span store tests
-	ingester.RunSpanStoreTests(t)
+			ingester.RunSpanStoreTests(t)
+		})
+	}
 }