diff --git a/test/e2e/generator/generate.go b/test/e2e/generator/generate.go
index 554384d97..1e134cf71 100644
--- a/test/e2e/generator/generate.go
+++ b/test/e2e/generator/generate.go
@@ -31,6 +31,7 @@ var (
 	nodePrivvalProtocols = uniformChoice{"file", "unix", "tcp", "grpc"}
 	// FIXME: v2 disabled due to flake
 	nodeFastSyncs         = uniformChoice{"v0"} // "v2"
+	nodeMempools          = uniformChoice{"v0", "v1"}
 	nodeStateSyncs        = uniformChoice{false, true}
 	nodePersistIntervals  = uniformChoice{0, 1, 5}
 	nodeSnapshotIntervals = uniformChoice{0, 3}
@@ -273,6 +274,7 @@ func generateNode(
 		ABCIProtocol:     nodeABCIProtocols.Choose(r).(string),
 		PrivvalProtocol:  nodePrivvalProtocols.Choose(r).(string),
 		FastSync:         nodeFastSyncs.Choose(r).(string),
+		Mempool:          nodeMempools.Choose(r).(string),
 		StateSync:        nodeStateSyncs.Choose(r).(bool) && startAt > 0,
 		PersistInterval:  ptrUint64(uint64(nodePersistIntervals.Choose(r).(int))),
 		SnapshotInterval: uint64(nodeSnapshotIntervals.Choose(r).(int)),
diff --git a/test/e2e/pkg/manifest.go b/test/e2e/pkg/manifest.go
index 5320c4637..89b38e02a 100644
--- a/test/e2e/pkg/manifest.go
+++ b/test/e2e/pkg/manifest.go
@@ -110,6 +110,9 @@ type ManifestNode struct {
 	// Defaults to disabled.
 	FastSync string `toml:"fast_sync"`
 
+	// Mempool specifies which version of mempool to use. Either "v0" or "v1"
+	Mempool string `toml:"mempool_version"`
+
 	// StateSync enables state sync. The runner automatically configures trusted
 	// block hashes and RPC servers. At least one node in the network must have
 	// SnapshotInterval set to non-zero, and the state syncing node must have
diff --git a/test/e2e/pkg/testnet.go b/test/e2e/pkg/testnet.go
index a5cec0147..d54df4406 100644
--- a/test/e2e/pkg/testnet.go
+++ b/test/e2e/pkg/testnet.go
@@ -80,6 +80,7 @@ type Node struct {
 	ProxyPort        uint32
 	StartAt          int64
 	FastSync         string
+	Mempool          string
 	StateSync        bool
 	Database         string
 	ABCIProtocol     Protocol
@@ -168,6 +169,7 @@ func LoadTestnet(file string) (*Testnet, error) {
 			PrivvalProtocol:  ProtocolFile,
 			StartAt:          nodeManifest.StartAt,
 			FastSync:         nodeManifest.FastSync,
+			Mempool:          nodeManifest.Mempool,
 			StateSync:        nodeManifest.StateSync,
 			PersistInterval:  1,
 			SnapshotInterval: nodeManifest.SnapshotInterval,
@@ -331,6 +333,11 @@ func (n Node) Validate(testnet Testnet) error {
 	default:
 		return fmt.Errorf("invalid fast sync setting %q", n.FastSync)
 	}
+	switch n.Mempool {
+	case "", "v0", "v1":
+	default:
+		return fmt.Errorf("invalid mempool version %q", n.Mempool)
+	}
 	switch n.QueueType {
 	case "", "priority", "wdrr", "fifo":
 	default:
diff --git a/test/e2e/runner/setup.go b/test/e2e/runner/setup.go
index c2b61617e..c80d05b22 100644
--- a/test/e2e/runner/setup.go
+++ b/test/e2e/runner/setup.go
@@ -292,6 +292,10 @@ func MakeConfig(node *e2e.Node) (*config.Config, error) {
 		return nil, fmt.Errorf("unexpected mode %q", node.Mode)
 	}
 
+	if node.Mempool != "" {
+		cfg.Mempool.Version = node.Mempool
+	}
+
 	if node.FastSync == "" {
 		cfg.FastSyncMode = false
 	} else {