diff --git a/.gitignore b/.gitignore
index 538198fc..c342f17a 100644
--- a/.gitignore
+++ b/.gitignore
@@ -85,5 +85,5 @@ tags
 # End of https://www.gitignore.io/api/go,vim,emacs,visualstudiocode
 ### kube cache ###
 .kube
-### kustomize image ###
-hack/.bin/kustomize
+.kustomize
+.controller-gen
diff --git a/Makefile b/Makefile
index a26fd5ab..03c98ef0 100644
--- a/Makefile
+++ b/Makefile
@@ -21,6 +21,9 @@ ifndef IS_CERTIFICATION
 	IS_CERTIFICATION=false
 endif
 
+.PHONY: all
+all: generate golangci manager
+
 include versioning.mk
 LDFLAGS += $(VERSION_LDFLAGS)
 
@@ -43,21 +46,24 @@ PKG_IS_DEFAULT_CHANNEL := --default-channel
 endif
 PKG_MAN_OPTS ?= $(FROM_VERSION) $(PKG_CHANNELS) $(PKG_IS_DEFAULT_CHANNEL)
 
-all: generate golangci manager
+GOLANGCI_LINT_VERSION := v1.51.0
+GOLANGCI_LINT_BINDIR  := $(CURDIR)/.golangci-bin
+GOLANGCI_LINT_BIN     := $(GOLANGCI_LINT_BINDIR)/$(GOLANGCI_LINT_VERSION)/golangci-lint
 
-.golangci-bin:
+$(GOLANGCI_LINT_BIN):
 	@echo "===> Installing Golangci-lint <==="
-	@curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $@ v1.51.0
+	@rm -rf $(GOLANGCI_LINT_BINDIR)/* # remove old versions
+	@curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $(GOLANGCI_LINT_BINDIR)/$(GOLANGCI_LINT_VERSION) $(GOLANGCI_LINT_VERSION)
 
 .PHONY: golangci
-golangci: .golangci-bin
+golangci: $(GOLANGCI_LINT_BIN)
 	@echo "===> Running golangci <==="
-	@GOOS=linux .golangci-bin/golangci-lint run -c .golangci.yml
+	@GOOS=linux $(GOLANGCI_LINT_BIN) run -c $(CURDIR)/.golangci.yml
 
 .PHONY: golangci-fix
-golangci-fix: .golangci-bin
-	@echo "===> Running golangci-fix<==="
-	@GOOS=linux .golangci-bin/golangci-lint run -c .golangci.yml --fix
+golangci-fix: $(GOLANGCI_LINT_BIN)
+	@echo "===> Running golangci-fix <==="
+	@GOOS=linux $(GOLANGCI_LINT_BIN) run -c $(CURDIR)/.golangci.yml --fix
 
 # Run tests
 ENVTEST_ASSETS_DIR = $(shell pwd)/testbin
@@ -102,29 +108,30 @@ docker-build:
 	docker build -f build/Dockerfile --label version="$(VERSION)" . -t ${IMG}
 	docker tag ${IMG} antrea/antrea-operator
 
-# find or download controller-gen
-# download controller-gen if necessary
-controller-gen:
-ifeq (, $(shell which controller-gen))
-	@{ \
-	set -e ;\
-	go install sigs.k8s.io/controller-tools/cmd/controller-gen@v0.6.2 ;\
-	}
-CONTROLLER_GEN=$(GOBIN)/controller-gen
-else
-CONTROLLER_GEN=$(shell which controller-gen)
-endif
+CONTROLLER_GEN_VERSION := v0.6.2
+CONTROLLER_GEN_BINDIR  := $(CURDIR)/.controller-gen
+CONTROLLER_GEN         := $(CONTROLLER_GEN_BINDIR)/$(CONTROLLER_GEN_VERSION)/controller-gen
 
-kustomize:
-ifeq (, $(shell which kustomize))
-	@{ \
-	set -e ;\
-	go install sigs.k8s.io/kustomize/kustomize/v5@v5.2.1 ;\
-	}
-KUSTOMIZE=$(GOBIN)/kustomize
-else
-KUSTOMIZE=$(shell which kustomize)
-endif
+$(CONTROLLER_GEN):
+	@echo "===> Installing Controller-gen  <==="
+	@rm -rf $(CONTROLLER_GEN_BINDIR)/* # remove old versions
+	GOBIN=$(CONTROLLER_GEN_BINDIR)/$(CONTROLLER_GEN_VERSION) go install sigs.k8s.io/controller-tools/cmd/controller-gen@$(CONTROLLER_GEN_VERSION)
+
+.PHONY: controller-gen
+controller-gen: $(CONTROLLER_GEN)
+
+KUSTOMIZE_VERSION := 5.3.0
+KUSTOMIZE_BINDIR  := $(CURDIR)/.kustomize
+KUSTOMIZE         := $(KUSTOMIZE_BINDIR)/$(KUSTOMIZE_VERSION)/kustomize
+
+$(KUSTOMIZE):
+	@echo "===> Installing Kustomize <==="
+	@rm -rf $(KUSTOMIZE_BINDIR)/* # remove old versions
+	@mkdir -p $(KUSTOMIZE_BINDIR)/$(KUSTOMIZE_VERSION)
+	@curl -sSfL https://raw.githubusercontent.com/kubernetes-sigs/kustomize/master/hack/install_kustomize.sh | bash -s -- $(KUSTOMIZE_VERSION) $(KUSTOMIZE_BINDIR)/$(KUSTOMIZE_VERSION)
+
+.PHONY: kustomize
+kustomize: $(KUSTOMIZE)
 
 # Generate bundle manifests and metadata, then validate generated files.
 .PHONY: bundle
@@ -156,7 +163,7 @@ bundle-build:
 	docker tag ${BUNDLE_IMG} antrea/antrea-operator-bundle
 
 antrea-resources:
-	./hack/generate-antrea-resources.sh --platform $(ANTREA_PLATFORM) --version $(VERSION)
+	KUSTOMIZE=$(KUSTOMIZE) ./hack/generate-antrea-resources.sh --platform $(ANTREA_PLATFORM) --version $(VERSION)
 	cp ./config/rbac/role.yaml ./deploy/$(ANTREA_PLATFORM)/role.yaml
 	cp ./config/samples/operator_v1_antreainstall.yaml ./deploy/$(ANTREA_PLATFORM)/operator.antrea.vmware.com_v1_antreainstall_cr.yaml
 
@@ -178,3 +185,10 @@ tidy:
 
 .PHONY: bin
 bin: manager
+
+.PHONY: clean
+clean:
+	@rm -rf bin
+	@rm -rf $(GOLANGCI_LINT_BINDIR)
+	@rm -rf $(KUSTOMIZE_BINDIR)
+	@rm -rf $(CONTROLLER_GEN_BINDIR)
diff --git a/antrea-manifest/antrea.yml b/antrea-manifest/antrea.yml
index f6305a1a..8ae6fcc9 100644
--- a/antrea-manifest/antrea.yml
+++ b/antrea-manifest/antrea.yml
@@ -6413,11 +6413,11 @@ subjects:
 apiVersion: v1
 data:
   antrea-agent.conf: |
-{{- .AntreaAgentConfig | nindent 4 }}
+    {{- .AntreaAgentConfig | nindent 4 }}
   antrea-cni.conflist: |
-{{- .AntreaCNIConfig | nindent 4 }}
+    {{- .AntreaCNIConfig | nindent 4 }}
   antrea-controller.conf: |
-{{- .AntreaControllerConfig | nindent 4 }}
+    {{- .AntreaControllerConfig | nindent 4 }}
 kind: ConfigMap
 metadata:
   labels:
diff --git a/hack/generate-antrea-resources.sh b/hack/generate-antrea-resources.sh
index 8dc6ddaf..ddf0f2ee 100755
--- a/hack/generate-antrea-resources.sh
+++ b/hack/generate-antrea-resources.sh
@@ -13,10 +13,8 @@ Generate a YAML manifest for Antrea using Kustomize and print it to stdout.
         --help, -h                    Print this message and exit
 
 This tool uses kustomize (https://github.com/kubernetes-sigs/kustomize) to generate manifests for
-Antrea. You can set the KUSTOMIZE environment variable to the path of the kustomize binary you want
-us to use. Otherwise we will download the appropriate version of the kustomize binary and use
-it (this is the recommended approach since different versions of kustomize may create different
-output YAMLs)."
+Antrea. You must set the KUSTOMIZE environment variable to the path of the kustomize binary you want
+us to use."
 
 function print_usage {
     echoerr "$_usage"
@@ -59,12 +57,8 @@ fi
 
 THIS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
 
-source $THIS_DIR/verify-kustomize.sh
-
 if [ -z "$KUSTOMIZE" ]; then
-    KUSTOMIZE="$(verify_kustomize)"
-elif ! $KUSTOMIZE version > /dev/null 2>&1; then
-    echoerr "$KUSTOMIZE does not appear to be a valid kustomize binary"
+    echoerr "KUSTOMIZE environment variable must be set"
     print_help
     exit 1
 fi
@@ -119,7 +113,7 @@ $KUSTOMIZE edit add patch --path controllerImage.yml
 $KUSTOMIZE edit add patch --path agentImagePullPolicy.yml
 $KUSTOMIZE edit add patch --path controllerImagePullPolicy.yml
 
-$KUSTOMIZE build | sed 's/^\s*{{/{{/; s/\\"\({{.*}}\)\\"/"\1"/; '"s/'\({{.*}}\)'/\1/" > $THIS_DIR/../antrea-manifest/antrea.yml
+$KUSTOMIZE build | sed 's/\\"\({{.*}}\)\\"/"\1"/; '"s/'\({{.*}}\)'/\1/" > $THIS_DIR/../antrea-manifest/antrea.yml
 
 popd > /dev/null
 
diff --git a/hack/verify-kustomize.sh b/hack/verify-kustomize.sh
deleted file mode 100644
index 0b61523d..00000000
--- a/hack/verify-kustomize.sh
+++ /dev/null
@@ -1,58 +0,0 @@
-#!/usr/bin/env bash
-
-# Copyright 2019 Antrea Authors
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-#     http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-THIS_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
-_BINDIR="$THIS_DIR/.bin"
-# Must be an exact match, as the generated YAMLs may not be consistent across
-# versions
-_KUSTOMIZE_VERSION="v4.4.1"
-
-# Ensure the kustomize tool exists and is the correct version, or installs it
-verify_kustomize() {
-    # Check if there is already a kustomize binary in $_BINDIR and if yes, check
-    # if the version matches the expected one.
-    local kustomize="$(PATH=$_BINDIR command -v kustomize)"
-    if [ -x "$kustomize" ]; then
-        # Verify version if kustomize was already installed.
-        local kustomize_version="$($kustomize version --short)"
-        kustomize_version="${kustomize_version##*/}"
-        kustomize_version="${kustomize_version%% *}"
-        if [ "${kustomize_version}" == "${_KUSTOMIZE_VERSION}" ]; then
-            # If version is exact match, stop here.
-            echo "$kustomize"
-            return 0
-        fi
-        >&2 echo "Detected kustomize version ($kustomize_version) does not match expected one ($_KUSTOMIZE_VERSION), installing correct version"
-    fi
-    local ostype=""
-    if [[ "$OSTYPE" == "linux-gnu" ]]; then
-        ostype="linux"
-    elif [[ "$OSTYPE" == "darwin"* ]]; then
-        ostype="darwin"
-    else
-        >&2 echo "Unsupported OS type $OSTYPE"
-        return 1
-    fi
-    >&2 echo "Installing kustomize"
-    local kustomize_url="https://github.com/kubernetes-sigs/kustomize/releases/download/kustomize/${_KUSTOMIZE_VERSION}/kustomize_${_KUSTOMIZE_VERSION}_${ostype}_amd64.tar.gz"
-    curl -sLo kustomize.tar.gz "${kustomize_url}" || return 1
-    mkdir -p "$_BINDIR" || return 1
-    tar -xzf kustomize.tar.gz -C "$_BINDIR" || return 1
-    rm -f kustomize.tar.gz
-    kustomize="$_BINDIR/kustomize"
-    echo "$kustomize"
-    return 0
-}