diff --git a/Makefile b/Makefile
index e82c2ca2..c8608e20 100644
--- a/Makefile
+++ b/Makefile
@@ -50,6 +50,7 @@ OCI_BIN_PATH := $(shell which docker 2>/dev/null || which podman)
 OCI_BIN ?= $(shell basename ${OCI_BIN_PATH})
 
 GOLANGCI_LINT_VERSION = v1.54.2
+YQ_VERSION = v4.43.1
 
 # build a single arch target provided as argument
 define build_target
@@ -82,6 +83,9 @@ prereqs: ## Test if prerequisites are met, and installing missing dependencies
 ifeq (, $(shell which golangci-lint))
 	GOFLAGS="" go install github.com/golangci/golangci-lint/cmd/golangci-lint@${GOLANGCI_LINT_VERSION}
 endif
+ifeq (, $(shell which yq))
+	GOFLAGS="" go install github.com/mikefarah/yq/v4@${YQ_VERSION}
+endif
 
 .PHONY: vendors
 vendors: ## Refresh vendors directory.
diff --git a/commands/netobserv-flows b/commands/netobserv-flows
index ec9ef9f9..2300c336 100755
--- a/commands/netobserv-flows
+++ b/commands/netobserv-flows
@@ -1,23 +1,13 @@
 #!/bin/bash
 source "./scripts/functions.sh"
 
-# interface filter such as 'br-ex'
-filter=""
-
-if [ -z "${1:-}" ]
-then
-  echo "Filters not set"
-else
-  echo "Filters set as $1"
-  filter=$1
-fi
-
 # CLI image to use
 img="quay.io/netobserv/network-observability-cli:main"
 
 trap cleanup EXIT
 
-setup flows $filter
+
+setup flows "$*"
 
 echo "Running network-observability-cli get-flows... "
 ${K8S_CLI_BIN} run \
@@ -35,4 +25,4 @@ ${K8S_CLI_BIN} wait \
 ${K8S_CLI_BIN} exec -i --tty \
   -n netobserv-cli \
   collector \
-  -- /network-observability-cli get-flows ${filter:+"--filter" "$filter"}
\ No newline at end of file
+  -- /network-observability-cli get-flows
\ No newline at end of file
diff --git a/res/flow-capture.yml b/res/flow-capture.yml
index 95677442..c0853b3f 100644
--- a/res/flow-capture.yml
+++ b/res/flow-capture.yml
@@ -30,7 +30,7 @@ spec:
           - name: LOG_LEVEL
             value: trace
           - name: INTERFACES
-            value: "{{FLOW_FILTER_VALUE}}"
+            value: ""
           - name: EXCLUDE_INTERFACES
             value: "lo"
           - name: SAMPLING
@@ -41,6 +41,34 @@ spec:
             value: "true"
           - name: ENABLE_DNS_TRACKING
             value: "true"
+          - name: ENABLE_FLOW_FILTER
+            value: ""
+          - name: FLOW_FILTER_DIRECTION
+            value: ""
+          - name: FLOW_FILTER_IP_CIDR
+            value: ""
+          - name: FLOW_FILTER_PROTOCOL
+            value: ""
+          - name: FLOW_FILTER_SOURCE_PORT
+            value: ""
+          - name: FLOW_FILTER_DESTINATION_PORT
+            value: ""
+          - name: FLOW_FILTER_PORT
+            value: ""
+          - name:  FLOW_FILTER_SOURCE_PORT_RANGE
+            value: ""
+          - name: FLOW_FILTER_DESTINATION_PORT_RANGE
+            value: ""
+          - name: FLOW_FILTER_PORT_RANGE
+            value: ""
+          - name: FLOW_FILTER_ICMP_TYPE
+            value: ""
+          - name: FLOW_FILTER_ICMP_CODE
+            value: ""
+          - name: FLOW_FILTER_PEER_IP
+            value: ""
+          - name: FLOW_FILTER_ACTION
+            value: ""
           - name: EXPORT
             value: "direct-flp"
           - name: FLP_CONFIG
diff --git a/scripts/functions.sh b/scripts/functions.sh
index cb533ace..60a428d9 100755
--- a/scripts/functions.sh
+++ b/scripts/functions.sh
@@ -1,4 +1,6 @@
 #!/usr/bin/env bash
+source ./scripts/update_flowcapture.sh
+
 set -eu
 
 # get either oc (favorite) or kubectl paths
@@ -22,13 +24,6 @@ function loadYAMLs() {
     saYAML="$(cat ./res/service-account.yml)"
   fi
 
-  flowAgentYAML='
-    flowAgentYAMLContent
-  '
-  if [ -f ./res/flow-capture.yml ]; then
-    flowAgentYAML="$(cat ./res/flow-capture.yml)"
-  fi
-
   packetAgentYAML='
     packetAgentYAMLContent
   '
@@ -57,6 +52,9 @@ function clusterIsReady() {
     fi
 }
 
+MANIFEST_FILE="flow-capture.yml"
+MANIFEST_OUTPUT_PATH="output"
+
 function setup {
   echo "Setting up... "
 
@@ -85,9 +83,71 @@ function setup {
   echo "$collectorServiceYAML" | ${K8S_CLI_BIN} apply -f -
 
   if [ "$1" = "flows" ]; then
-    echo "creating flow-capture agents"
-    echo "${flowAgentYAML/"{{FLOW_FILTER_VALUE}}"/${2:-}}" | ${K8S_CLI_BIN} apply -f -
-    ${K8S_CLI_BIN} rollout status daemonset netobserv-cli -n netobserv-cli --timeout 60s
+    shift
+    echo "creating flow-capture agents:"
+    options="$*"
+    # Iterate through the command-line arguments
+    for option in $options; do
+        key="${option%%=*}"
+        value="${option#*=}"
+        case "$key" in
+            --interfaces) # Interfaces
+                edit_manifest "interfaces" "$value"
+                ;;
+            --enable) # Enable flow filter
+                edit_manifest "filter_enable" "$value"
+                ;;
+            --direction) # Configure flow filter direction
+                edit_manifest "filter_direction" "$value"
+                ;;
+            --cidr) # Configure flow filter CIDR
+                edit_manifest "filter_cidr" "$value"
+                ;;
+            --protocol) # Configure flow filter protocol
+                edit_manifest "filter_protocol" "$value"
+                ;;
+            --sport) # Configure flow filter source port
+                edit_manifest "filter_src_port" "$value"
+                ;;
+            --dport) # Configure flow filter destination port
+                edit_manifest "filter_dst_port" "$value"
+                ;;
+            --port) # Configure flow filter port
+                edit_manifest "filter_port" "$value"
+                ;;
+            --sport-range) # Configure flow filter source port range
+                edit_manifest "filter_src_port_range" "$value"
+                ;;
+            --dport-range) # Configure flow filter destination port range
+                edit_manifest "filter_dst_port_range" "$value"
+                ;;
+            --port-range) # Configure flow filter port range
+                edit_manifest "filter_port_range" "$value"
+                ;;
+            --icmp-type) # ICMP type
+                edit_manifest "filter_icmp_type" "$value"
+                ;;
+            --icmp-code) # ICMP code
+                edit_manifest "filter_icmp_code" "$value"
+                ;;
+            --peer-ip) # Peer IP
+                edit_manifest "filter_peer_ip" "$value"
+                ;;
+            --action) # Filter action
+                edit_manifest "filter_action" "$value"
+                ;;
+            *) # Invalid option
+                echo "Invalid option: $key" >&2
+                exit 1
+                ;;
+        esac
+    done
+
+    manifest="$MANIFEST_OUTPUT_PATH"/"$MANIFEST_FILE"
+    if [[ -f "$manifest" ]]; then
+      ${K8S_CLI_BIN}   apply -f "$manifest"
+      ${K8S_CLI_BIN}  rollout status daemonset netobserv-cli -n netobserv-cli --timeout 60s
+    fi
   elif [ "$1" = "packets" ]; then
     echo "creating packet-capture agents"
     echo "${packetAgentYAML/"{{PCA_FILTER_VALUE}}"/${2:-}}" | ${K8S_CLI_BIN} apply -f -
diff --git a/scripts/update_flowcapture.sh b/scripts/update_flowcapture.sh
new file mode 100755
index 00000000..2b9e301b
--- /dev/null
+++ b/scripts/update_flowcapture.sh
@@ -0,0 +1,62 @@
+#!/bin/bash
+
+MANIFEST_FILE="flow-capture.yml"
+MANIFEST_PATH="res"
+MANIFEST_OUTPUT_PATH="output"
+
+function edit_manifest() {
+  echo "Editing manifest file..."
+  if [[ ! -d ${MANIFEST_OUTPUT_PATH} ]]; then
+    mkdir -p ${MANIFEST_OUTPUT_PATH} > /dev/null
+    cp ${MANIFEST_PATH}/${MANIFEST_FILE} ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+  fi
+  ## replace the env variable in the manifest file
+  echo "env: $1, env_value: $2"
+  case "$1" in
+  "interfaces")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"INTERFACES\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_enable")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"ENABLE_FLOW_FILTER\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_direction")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_DIRECTION\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_cidr")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_IP_CIDR\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_protocol")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_PROTOCOL\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_sport")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_SOURCE_PORT\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_dport")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_DESTINATION_PORT\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_port")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_PORT\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_sport_range")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_SOURCE_PORT_RANGE\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_dport_range")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_DESTINATION_PORT_RANGE\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_port_range")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_PORT_RANGE\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_icmp_type")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_ICMP_TYPE\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_icmp_code")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_ICMP_CODE\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_peer_ip")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_PEER_IP\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  "filter_action")
+    yq e --inplace ".spec.template.spec.containers[0].env[] |= select(.name==\"FLOW_FILTER_ACTION\").value|=\"$2\"" ${MANIFEST_OUTPUT_PATH}/${MANIFEST_FILE}
+    ;;
+  esac
+}