diff --git a/zombienet_tests/README.md b/zombienet_tests/README.md
index 021d3643e7f9..5a4c97355f09 100644
--- a/zombienet_tests/README.md
+++ b/zombienet_tests/README.md
@@ -25,7 +25,7 @@ To run any test locally use the native provider (`zombienet test -p native ...`)
 To build them use:
 * adder-collator -> `cargo build --profile testnet -p test-parachain-adder-collator`
 * undying-collator -> `cargo build --profile testnet -p test-parachain-undying-collator`
-* malus -> cargo build --profile testnet -p polkadot-test-malus
+* malus -> `cargo build --profile testnet -p polkadot-test-malus`
 * polkadot (in polkadot repo) and polkadot-collator (in cumulus repo) -> `cargo build --profile testnet`
 
 One solution is to use the `.set_env` file (from this directory) and fill the `CUSTOM_PATHS` before *source* it to patch the PATH of your system to find the binaries you just built.
diff --git a/zombienet_tests/functional/0003-beefy-and-mmr.toml b/zombienet_tests/functional/0003-beefy-and-mmr.toml
index 1608976abdf2..bea5ac1ba64f 100644
--- a/zombienet_tests/functional/0003-beefy-and-mmr.toml
+++ b/zombienet_tests/functional/0003-beefy-and-mmr.toml
@@ -8,5 +8,9 @@ command = "polkadot"
 
 [[relaychain.node_groups]]
 name = "validator"
-count = 4
+count = 3
+args = ["--log=beefy=debug", "--beefy", "--enable-offchain-indexing=true"]
+
+[[relaychain.nodes]]
+name = "validator-unstable"
 args = ["--log=beefy=debug", "--beefy", "--enable-offchain-indexing=true"]
diff --git a/zombienet_tests/functional/0003-beefy-and-mmr.zndsl b/zombienet_tests/functional/0003-beefy-and-mmr.zndsl
index c927a671658d..8300ef051f09 100644
--- a/zombienet_tests/functional/0003-beefy-and-mmr.zndsl
+++ b/zombienet_tests/functional/0003-beefy-and-mmr.zndsl
@@ -3,45 +3,37 @@ Network: ./0003-beefy-and-mmr.toml
 Creds: config
 
 # Check authority status.
-validator-0: reports node_roles is 4
-validator-1: reports node_roles is 4
-validator-2: reports node_roles is 4
-validator-3: reports node_roles is 4
+validator: reports node_roles is 4
+validator-unstable: reports node_roles is 4
 
 # BEEFY sanity checks.
-validator-0: reports substrate_beefy_validator_set_id is 0
-validator-1: reports substrate_beefy_validator_set_id is 0
-validator-2: reports substrate_beefy_validator_set_id is 0
-validator-3: reports substrate_beefy_validator_set_id is 0
+validator: reports substrate_beefy_validator_set_id is 0
+validator-unstable: reports substrate_beefy_validator_set_id is 0
 
 # Verify voting happens and 1st mandatory block is finalized within 1st session.
-validator-0: reports substrate_beefy_best_block is at least 1 within 60 seconds
-validator-1: reports substrate_beefy_best_block is at least 1 within 60 seconds
-validator-2: reports substrate_beefy_best_block is at least 1 within 60 seconds
-validator-3: reports substrate_beefy_best_block is at least 1 within 60 seconds
+validator: reports substrate_beefy_best_block is at least 1 within 60 seconds
+validator-unstable: reports substrate_beefy_best_block is at least 1 within 60 seconds
 
-# Pause validator-3 and test chain is making progress without it.
-validator-3: pause
+# Pause validator-unstable and test chain is making progress without it.
+validator-unstable: pause
 
 # Verify validator sets get changed on new sessions.
-validator-0: reports substrate_beefy_validator_set_id is at least 1 within 70 seconds
-validator-1: reports substrate_beefy_validator_set_id is at least 1 within 70 seconds
-validator-2: reports substrate_beefy_validator_set_id is at least 1 within 70 seconds
+validator: reports substrate_beefy_validator_set_id is at least 1 within 70 seconds
 # Check next session too.
-validator-0: reports substrate_beefy_validator_set_id is at least 2 within 130 seconds
-validator-1: reports substrate_beefy_validator_set_id is at least 2 within 130 seconds
-validator-2: reports substrate_beefy_validator_set_id is at least 2 within 130 seconds
+validator: reports substrate_beefy_validator_set_id is at least 2 within 130 seconds
 
 # Verify voting happens and blocks are being finalized for new sessions too:
 # since we verified we're at least in the 3rd session, verify BEEFY finalized mandatory #21.
-validator-0: reports substrate_beefy_best_block is at least 21 within 130 seconds
-validator-1: reports substrate_beefy_best_block is at least 21 within 130 seconds
-validator-2: reports substrate_beefy_best_block is at least 21 within 130 seconds
+validator: reports substrate_beefy_best_block is at least 21 within 130 seconds
 
-# TODO (issue #11972): Custom JS to test BEEFY RPCs
-# TODO (issue #11972): Custom JS to test MMR RPCs
+# Custom JS to test BEEFY RPCs.
+validator-0: js-script ./0003-beefy-finalized-heads.js with "validator-0,validator-1,validator-2" return is 1 within 5 seconds
 
-# Resume validator-3 and verify it imports all BEEFY justification and catches up.
-validator-3: resume
-validator-3: reports substrate_beefy_validator_set_id is at least 2 within 30 seconds
-validator-3: reports substrate_beefy_best_block is at least 21 within 30 seconds
+# Custom JS to test MMR RPCs.
+validator: js-script ./0003-mmr-leaves.js with "21" return is 1 within 5 seconds
+validator: js-script ./0003-mmr-generate-and-verify-proof.js with "validator-0,validator-1,validator-2" return is 1 within 5 seconds
+
+# Resume validator-unstable and verify it imports all BEEFY justification and catches up.
+validator-unstable: resume
+validator-unstable: reports substrate_beefy_validator_set_id is at least 2 within 30 seconds
+validator-unstable: reports substrate_beefy_best_block is at least 21 within 30 seconds
diff --git a/zombienet_tests/functional/0003-beefy-finalized-heads.js b/zombienet_tests/functional/0003-beefy-finalized-heads.js
new file mode 100644
index 000000000000..9696a540a18c
--- /dev/null
+++ b/zombienet_tests/functional/0003-beefy-finalized-heads.js
@@ -0,0 +1,35 @@
+const common = require('./0003-common.js');
+
+async function run(_, networkInfo, nodeNames) {
+  const apis = await common.getApis(networkInfo, nodeNames);
+
+  const finalizedHeads = await Promise.all(
+    Object.entries(apis).map(async ([nodeName, api]) => {
+      const finalizedHead = await api.rpc.beefy.getFinalizedHead();
+      return { nodeName, finalizedHead, finalizedHeight: await api.rpc.chain.getHeader(finalizedHead).then((header) => header.number) };
+    })
+  );
+
+  // select the node with the highest finalized height
+  const highestFinalizedHeight = finalizedHeads.reduce(
+    (acc, { nodeName, finalizedHeight }) =>
+      finalizedHeight >= acc.finalizedHeight
+        ? { nodeName, finalizedHeight }
+        : acc,
+    { nodeName: 'validator', finalizedHeight: 0 }
+  );
+
+  // get all block hashes up until the highest finalized height
+  const blockHashes = [];
+  for (let blockNumber = 0; blockNumber <= highestFinalizedHeight.finalizedHeight; blockNumber++) {
+    const blockHash = await apis[highestFinalizedHeight.nodeName].rpc.chain.getBlockHash(blockNumber);
+    blockHashes.push(blockHash);
+  }
+
+  // verify that height(finalized_head) is at least as high as the substrate_beefy_best_block test already verified
+  return finalizedHeads.every(({ finalizedHead, finalizedHeight }) =>
+    finalizedHeight >= 21 && finalizedHead.toHex() === blockHashes[finalizedHeight].toHex()
+  )
+}
+
+module.exports = { run };
diff --git a/zombienet_tests/functional/0003-common.js b/zombienet_tests/functional/0003-common.js
new file mode 100644
index 000000000000..743828ec6b9e
--- /dev/null
+++ b/zombienet_tests/functional/0003-common.js
@@ -0,0 +1,16 @@
+async function getApis(networkInfo, nodeNames) {
+  const connectionPromises = nodeNames.map(async (nodeName) => {
+    const { wsUri, userDefinedTypes } = networkInfo.nodesByName[nodeName];
+    const connection = await zombie.connect(wsUri, userDefinedTypes);
+    return { nodeName, connection };
+  });
+
+  const connections = await Promise.all(connectionPromises);
+
+  return connections.reduce((map, { nodeName, connection }) => {
+    map[nodeName] = connection;
+    return map;
+  }, {});
+}
+
+module.exports = { getApis };
diff --git a/zombienet_tests/functional/0003-mmr-generate-and-verify-proof.js b/zombienet_tests/functional/0003-mmr-generate-and-verify-proof.js
new file mode 100644
index 000000000000..6583173e40c3
--- /dev/null
+++ b/zombienet_tests/functional/0003-mmr-generate-and-verify-proof.js
@@ -0,0 +1,26 @@
+const common = require('./0003-common.js');
+
+async function run(nodeName, networkInfo, nodeNames) {
+  const apis = await common.getApis(networkInfo, nodeNames);
+
+  const proof = await apis[nodeName].rpc.mmr.generateProof([1, 9, 20]);
+
+  const root = await apis[nodeName].rpc.mmr.root()
+
+  const proofVerifications = await Promise.all(
+    Object.values(apis).map(async (api) => {
+      return api.rpc.mmr.verifyProof(proof);
+    })
+  );
+
+  const proofVerificationsStateless = await Promise.all(
+    Object.values(apis).map(async (api) => {
+      return api.rpc.mmr.verifyProofStateless(root, proof);
+    })
+  );
+
+  // check that all nodes accepted the proof
+  return proofVerifications.every((proofVerification) => proofVerification) && proofVerificationsStateless.every((proofVerification) => proofVerification)
+}
+
+module.exports = { run };
diff --git a/zombienet_tests/functional/0003-mmr-leaves.js b/zombienet_tests/functional/0003-mmr-leaves.js
new file mode 100644
index 000000000000..df58194c5769
--- /dev/null
+++ b/zombienet_tests/functional/0003-mmr-leaves.js
@@ -0,0 +1,9 @@
+async function run(nodeName, networkInfo, args) {
+  const { wsUri, userDefinedTypes } = networkInfo.nodesByName[nodeName];
+  const api = await zombie.connect(wsUri, userDefinedTypes);
+
+  const mmrLeaves = await api.query.mmr.numberOfLeaves();
+  return mmrLeaves.toNumber() >= args[0]
+}
+
+module.exports = { run };