diff --git a/yarn-project/aztec/src/cli/aztec_start_options.ts b/yarn-project/aztec/src/cli/aztec_start_options.ts
index 26d3f88df3f..bdd9229bb15 100644
--- a/yarn-project/aztec/src/cli/aztec_start_options.ts
+++ b/yarn-project/aztec/src/cli/aztec_start_options.ts
@@ -3,6 +3,7 @@ import { sequencerClientConfigMappings } from '@aztec/aztec-node';
 import { botConfigMappings } from '@aztec/bot';
 import {
   type ConfigMapping,
+  type EnvVar,
   booleanConfigHelper,
   filterConfigMappings,
   isBooleanConfigValue,
@@ -21,7 +22,7 @@ export interface AztecStartOption {
   description: string;
   defaultValue: any | undefined;
   printDefault?: (val: any) => string;
-  envVar: string | undefined;
+  envVar: EnvVar | undefined;
   parseVal?: (val: string) => any;
 }
 
@@ -45,7 +46,7 @@ export const getOptions = (namespace: string, configMappings: Record<string, Con
 };
 
 // These are options used by multiple modules so should be inputted once
-export const universalOptions = ['l1RpcUrl', 'l1ChainId', 'l1Contracts', 'p2pEnabled'];
+export const universalOptions = ['l1RpcUrl', 'l1ChainId', 'l1Contracts', 'p2pEnabled', 'dataDirectory'];
 
 // Define categories and options
 export const aztecStartOptions: { [key: string]: AztecStartOption[] } = {
@@ -158,16 +159,16 @@ export const aztecStartOptions: { [key: string]: AztecStartOption[] } = {
       envVar: undefined,
     },
     {
-      flag: '--node.archiverUrl <value>',
-      description: 'URL for an archiver service',
+      flag: '--data-directory <value>',
+      description: 'Where to store data. If not set, will store temporarily',
       defaultValue: undefined,
-      envVar: 'ARCHIVER_URL',
+      envVar: 'DATA_DIRECTORY',
     },
     {
-      flag: '--node.dataDirectory <value>',
-      description: 'Where to store node data. If not set, will store temporarily',
+      flag: '--node.archiverUrl <value>',
+      description: 'URL for an archiver service',
       defaultValue: undefined,
-      envVar: 'NODE_DATA_DIRECTORY',
+      envVar: 'ARCHIVER_URL',
     },
     {
       flag: '--node.deployAztecContracts',
@@ -221,6 +222,12 @@ export const aztecStartOptions: { [key: string]: AztecStartOption[] } = {
       defaultValue: undefined,
       envVar: undefined,
     },
+    {
+      flag: '--pxe.dataDirectory <value>',
+      description: 'Where to store PXE data. If not set, will store in memory',
+      defaultValue: undefined,
+      envVar: 'PXE_DATA_DIRECTORY',
+    },
     ...getOptions('pxe', allPxeConfigMappings),
   ],
   ARCHIVER: [
diff --git a/yarn-project/aztec/src/cli/cmds/start_archiver.ts b/yarn-project/aztec/src/cli/cmds/start_archiver.ts
index ff3690ae66d..95ad83b9972 100644
--- a/yarn-project/aztec/src/cli/cmds/start_archiver.ts
+++ b/yarn-project/aztec/src/cli/cmds/start_archiver.ts
@@ -18,7 +18,7 @@ import { extractRelevantOptions } from '../util.js';
 export const startArchiver = async (options: any, signalHandlers: (() => Promise<void>)[]) => {
   const services: ServerList = [];
   // Start a standalone archiver.
-  const archiverConfig = extractRelevantOptions<ArchiverConfig>(options, archiverConfigMappings);
+  const archiverConfig = extractRelevantOptions<ArchiverConfig>(options, archiverConfigMappings, 'archiver');
 
   const storeLog = createDebugLogger('aztec:archiver:lmdb');
   const rollupAddress = archiverConfig.l1Contracts.rollupAddress;
diff --git a/yarn-project/aztec/src/cli/cmds/start_bot.ts b/yarn-project/aztec/src/cli/cmds/start_bot.ts
index 4d45dd4e0db..cf61ed0aa95 100644
--- a/yarn-project/aztec/src/cli/cmds/start_bot.ts
+++ b/yarn-project/aztec/src/cli/cmds/start_bot.ts
@@ -37,7 +37,7 @@ export function addBot(
   signalHandlers: (() => Promise<void>)[],
   deps: { pxe?: PXE; node?: AztecNode } = {},
 ) {
-  const config = extractRelevantOptions<BotConfig>(options, botConfigMappings);
+  const config = extractRelevantOptions<BotConfig>(options, botConfigMappings, 'bot');
 
   const botRunner = new BotRunner(config, deps);
   const botServer = createBotRunnerRpcServer(botRunner);
diff --git a/yarn-project/aztec/src/cli/cmds/start_node.ts b/yarn-project/aztec/src/cli/cmds/start_node.ts
index 9748e4f57e1..b4279d7b2d7 100644
--- a/yarn-project/aztec/src/cli/cmds/start_node.ts
+++ b/yarn-project/aztec/src/cli/cmds/start_node.ts
@@ -27,7 +27,7 @@ export const startNode = async (
   const nodeSpecificOptions = extractNamespacedOptions(options, 'node');
   // All options that are relevant to the Aztec Node
   const nodeConfig = {
-    ...extractRelevantOptions(options, aztecNodeConfigMappings),
+    ...extractRelevantOptions(options, aztecNodeConfigMappings, 'node'),
     l1Contracts: extractL1ContractAddresses(options),
   };
 
@@ -90,7 +90,7 @@ export const startNode = async (
     }
   }
 
-  const telemetryConfig = extractRelevantOptions<TelemetryClientConfig>(options, telemetryClientConfigMappings);
+  const telemetryConfig = extractRelevantOptions<TelemetryClientConfig>(options, telemetryClientConfigMappings, 'tel');
   const telemetryClient = createAndStartTelemetryClient(telemetryConfig);
 
   // Create and start Aztec Node.
diff --git a/yarn-project/aztec/src/cli/cmds/start_p2p_bootstrap.ts b/yarn-project/aztec/src/cli/cmds/start_p2p_bootstrap.ts
index c2d57597e39..60ffada5411 100644
--- a/yarn-project/aztec/src/cli/cmds/start_p2p_bootstrap.ts
+++ b/yarn-project/aztec/src/cli/cmds/start_p2p_bootstrap.ts
@@ -7,7 +7,7 @@ import { extractRelevantOptions } from '../util.js';
 
 export const startP2PBootstrap = async (options: any, userLog: LogFn, debugLogger: DebugLogger) => {
   // Start a P2P bootstrap node.
-  const config = extractRelevantOptions<BootnodeConfig>(options, bootnodeConfigMappings);
+  const config = extractRelevantOptions<BootnodeConfig>(options, bootnodeConfigMappings, 'p2p');
   await runBootstrapNode(config, debugLogger);
   userLog(`P2P bootstrap node started on ${config.udpListenAddress}`);
 };
diff --git a/yarn-project/aztec/src/cli/cmds/start_prover_agent.ts b/yarn-project/aztec/src/cli/cmds/start_prover_agent.ts
index 1c71b49de8e..f6c73503816 100644
--- a/yarn-project/aztec/src/cli/cmds/start_prover_agent.ts
+++ b/yarn-project/aztec/src/cli/cmds/start_prover_agent.ts
@@ -11,7 +11,7 @@ import {
 import { type ServiceStarter, extractRelevantOptions } from '../util.js';
 
 export const startProverAgent: ServiceStarter = async (options, signalHandlers, logger) => {
-  const proverConfig = extractRelevantOptions<ProverClientConfig>(options, proverClientConfigMappings);
+  const proverConfig = extractRelevantOptions<ProverClientConfig>(options, proverClientConfigMappings, 'prover');
 
   if (!proverConfig.nodeUrl) {
     throw new Error('Starting prover without an orchestrator is not supported');
@@ -20,7 +20,7 @@ export const startProverAgent: ServiceStarter = async (options, signalHandlers,
   logger(`Connecting to prover at ${proverConfig.nodeUrl}`);
   const source = createProvingJobSourceClient(proverConfig.nodeUrl, 'provingJobSource');
 
-  const telemetryConfig = extractRelevantOptions<TelemetryClientConfig>(options, telemetryClientConfigMappings);
+  const telemetryConfig = extractRelevantOptions<TelemetryClientConfig>(options, telemetryClientConfigMappings, 'tel');
   const telemetry = createAndStartTelemetryClient(telemetryConfig);
 
   let circuitProver: ServerCircuitProver;
diff --git a/yarn-project/aztec/src/cli/cmds/start_prover_node.ts b/yarn-project/aztec/src/cli/cmds/start_prover_node.ts
index 8b0017c7a81..1c22e3d7308 100644
--- a/yarn-project/aztec/src/cli/cmds/start_prover_node.ts
+++ b/yarn-project/aztec/src/cli/cmds/start_prover_node.ts
@@ -32,7 +32,7 @@ export const startProverNode = async (
   }
 
   const proverConfig = {
-    ...extractRelevantOptions<ProverNodeConfig>(options, proverNodeConfigMappings),
+    ...extractRelevantOptions<ProverNodeConfig>(options, proverNodeConfigMappings, 'proverNode'),
     l1Contracts: extractL1ContractAddresses(options),
   };
 
diff --git a/yarn-project/aztec/src/cli/cmds/start_pxe.ts b/yarn-project/aztec/src/cli/cmds/start_pxe.ts
index 60bd6d52899..674657fd303 100644
--- a/yarn-project/aztec/src/cli/cmds/start_pxe.ts
+++ b/yarn-project/aztec/src/cli/cmds/start_pxe.ts
@@ -47,7 +47,7 @@ export async function addPXE(
   userLog: LogFn,
   deps: { node?: AztecNode } = {},
 ) {
-  const pxeConfig = extractRelevantOptions<PXEServiceConfig & CliPXEOptions>(options, allPxeConfigMappings);
+  const pxeConfig = extractRelevantOptions<PXEServiceConfig & CliPXEOptions>(options, allPxeConfigMappings, 'pxe');
 
   let nodeUrl;
   if (pxeConfig.network) {
diff --git a/yarn-project/aztec/src/cli/util.ts b/yarn-project/aztec/src/cli/util.ts
index ba6838fc9b8..cfdaaec236a 100644
--- a/yarn-project/aztec/src/cli/util.ts
+++ b/yarn-project/aztec/src/cli/util.ts
@@ -198,17 +198,39 @@ export const extractL1ContractAddresses = (options: Record<string, any>): L1Cont
  * @template T - The type of the relevant options.
  * @param options - Key-value map of options.
  * @param mappings - The mappings to extract.
+ * @param namespace - The namespace to extract for.
  * @returns Key-value map of relevant options.
  */
-export const extractRelevantOptions = <T>(options: Record<string, any>, mappings: ConfigMappingsType<T>): T => {
+export const extractRelevantOptions = <T>(
+  options: Record<string, any>,
+  mappings: ConfigMappingsType<T>,
+  namespace: string,
+): T => {
   const relevantOptions: T = {} as T;
 
-  Object.keys(options).forEach(key => {
-    const keyParts = key.split('.');
+  // Iterate over each key in the options
+  Object.keys(options).forEach(optionKey => {
+    const keyParts = optionKey.split('.');
+    const optionNamespace = keyParts.length > 1 ? keyParts[0] : '';
     const mainKey = keyParts.length > 1 ? keyParts[1] : keyParts[0];
 
+    // Check if the key exists in the mappings
     if (mainKey in mappings) {
-      relevantOptions[mainKey as keyof T] = options[key];
+      // Check for duplicates in the options
+      const duplicates = Object.keys(options).filter(optKey => {
+        const optKeyParts = optKey.split('.');
+        return optKeyParts[1] === mainKey || optKeyParts[0] === mainKey;
+      });
+
+      // If duplicates are found, use the namespace to differentiate
+      if (duplicates.length > 1) {
+        if (namespace === optionNamespace) {
+          relevantOptions[mainKey as keyof T] = options[optionKey];
+        }
+      } else {
+        // If no duplicates, extract the value without considering the namespace
+        relevantOptions[mainKey as keyof T] = options[optionKey];
+      }
     }
   });
 
diff --git a/yarn-project/foundation/src/config/env_var.ts b/yarn-project/foundation/src/config/env_var.ts
index 10c3c4a22f8..ea5027b309a 100644
--- a/yarn-project/foundation/src/config/env_var.ts
+++ b/yarn-project/foundation/src/config/env_var.ts
@@ -1,4 +1,6 @@
 export type EnvVar =
+  | 'AZTEC_PORT'
+  | 'ASSUME_PROVEN_UNTIL_BLOCK_NUMBER'
   | 'TEST_ACCOUNTS'
   | 'ENABLE_GAS'
   | 'API_PREFIX'