diff --git a/Cargo.lock b/Cargo.lock
index fb45da50..a763d686 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -3030,7 +3030,7 @@ dependencies = [
  "git2",
  "itertools 0.14.0",
  "serde_json",
- "serde_yaml 0.8.26",
+ "serde_yaml 0.9.34+deprecated",
  "shared-memory-server",
  "sysinfo 0.30.13",
  "tokio",
@@ -3161,7 +3161,7 @@ dependencies = [
  "futures-concurrency",
  "futures-timer",
  "serde_json",
- "serde_yaml 0.8.26",
+ "serde_yaml 0.9.34+deprecated",
  "shared-memory-server",
  "shared_memory_extended",
  "tokio",
@@ -3212,7 +3212,7 @@ dependencies = [
  "futures",
  "pyo3",
  "pythonize",
- "serde_yaml 0.8.26",
+ "serde_yaml 0.9.34+deprecated",
  "tokio",
 ]
 
@@ -3293,7 +3293,7 @@ dependencies = [
  "futures",
  "futures-concurrency",
  "pyo3",
- "serde_yaml 0.8.26",
+ "serde_yaml 0.9.34+deprecated",
 ]
 
 [[package]]
@@ -3419,7 +3419,7 @@ dependencies = [
  "libloading 0.7.4",
  "pyo3",
  "pythonize",
- "serde_yaml 0.8.26",
+ "serde_yaml 0.9.34+deprecated",
  "tokio",
  "tokio-stream",
  "tracing",
diff --git a/Cargo.toml b/Cargo.toml
index 541d3297..2b863fe5 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -93,6 +93,7 @@ pyo3 = { version = "0.23", features = [
 ] }
 pythonize = "0.23"
 git2 = { version = "0.18.0", features = ["vendored-openssl"] }
+serde_yaml = "0.9.33"
 
 [package]
 name = "dora-examples"
diff --git a/apis/python/node/Cargo.toml b/apis/python/node/Cargo.toml
index c06fbbaa..063d8157 100644
--- a/apis/python/node/Cargo.toml
+++ b/apis/python/node/Cargo.toml
@@ -21,7 +21,7 @@ dora-node-api = { workspace = true }
 dora-operator-api-python = { workspace = true }
 pyo3.workspace = true
 eyre = "0.6"
-serde_yaml = "0.8.23"
+serde_yaml = { workspace = true }
 flume = "0.10.14"
 dora-runtime = { workspace = true, features = ["tracing", "metrics", "python"] }
 dora-cli = { workspace = true }
diff --git a/apis/python/operator/Cargo.toml b/apis/python/operator/Cargo.toml
index a96c5987..a65a929d 100644
--- a/apis/python/operator/Cargo.toml
+++ b/apis/python/operator/Cargo.toml
@@ -14,7 +14,7 @@ repository.workspace = true
 dora-node-api = { workspace = true }
 pyo3 = { workspace = true, features = ["eyre", "abi3-py37"] }
 eyre = "0.6"
-serde_yaml = "0.8.23"
+serde_yaml = { workspace = true }
 flume = "0.10.14"
 arrow = { workspace = true, features = ["pyarrow"] }
 arrow-schema = { workspace = true }
diff --git a/apis/rust/node/Cargo.toml b/apis/rust/node/Cargo.toml
index a96256f0..d1485b4b 100644
--- a/apis/rust/node/Cargo.toml
+++ b/apis/rust/node/Cargo.toml
@@ -17,7 +17,7 @@ dora-core = { workspace = true }
 dora-message = { workspace = true }
 shared-memory-server = { workspace = true }
 eyre = "0.6.7"
-serde_yaml = "0.8.23"
+serde_yaml = { workspace = true }
 tracing = "0.1.33"
 flume = "0.10.14"
 bincode = "1.3.3"
diff --git a/apis/rust/node/src/node/mod.rs b/apis/rust/node/src/node/mod.rs
index 47890d46..af58e536 100644
--- a/apis/rust/node/src/node/mod.rs
+++ b/apis/rust/node/src/node/mod.rs
@@ -60,7 +60,7 @@ pub struct DoraNode {
     drop_stream: DropStream,
     cache: VecDeque<ShmemHandle>,
 
-    dataflow_descriptor: Descriptor,
+    dataflow_descriptor: serde_yaml::Result<Descriptor>,
     warned_unknown_output: BTreeSet<DataId>,
     _rt: TokioRuntime,
 }
@@ -200,7 +200,7 @@ impl DoraNode {
             sent_out_shared_memory: HashMap::new(),
             drop_stream,
             cache: VecDeque::new(),
-            dataflow_descriptor,
+            dataflow_descriptor: serde_yaml::from_value(dataflow_descriptor),
             warned_unknown_output: BTreeSet::new(),
             _rt: rt,
         };
@@ -449,8 +449,15 @@ impl DoraNode {
     /// Returns the full dataflow descriptor that this node is part of.
     ///
     /// This method returns the parsed dataflow YAML file.
-    pub fn dataflow_descriptor(&self) -> &Descriptor {
-        &self.dataflow_descriptor
+    pub fn dataflow_descriptor(&self) -> eyre::Result<&Descriptor> {
+        match &self.dataflow_descriptor {
+            Ok(d) => Ok(d),
+            Err(err) => eyre::bail!(
+                "failed to parse dataflow descriptor: {err}\n\n
+                This might be caused by mismatched version numbers of dora \
+                daemon and the dora node API"
+            ),
+        }
     }
 }
 
diff --git a/binaries/cli/Cargo.toml b/binaries/cli/Cargo.toml
index 51e07f54..e806dc60 100644
--- a/binaries/cli/Cargo.toml
+++ b/binaries/cli/Cargo.toml
@@ -27,7 +27,7 @@ dora-node-api-c = { workspace = true }
 dora-operator-api-c = { workspace = true }
 dora-download = { workspace = true }
 serde = { version = "1.0.136", features = ["derive"] }
-serde_yaml = "0.9.11"
+serde_yaml = { workspace = true }
 webbrowser = "0.8.3"
 serde_json = "1.0.86"
 termcolor = "1.1.3"
diff --git a/binaries/daemon/Cargo.toml b/binaries/daemon/Cargo.toml
index fdfd3596..04043b2f 100644
--- a/binaries/daemon/Cargo.toml
+++ b/binaries/daemon/Cargo.toml
@@ -31,7 +31,7 @@ dora-tracing = { workspace = true, optional = true }
 dora-arrow-convert = { workspace = true }
 dora-node-api = { workspace = true }
 dora-message = { workspace = true }
-serde_yaml = "0.8.23"
+serde_yaml = { workspace = true }
 uuid = { version = "1.7", features = ["v7"] }
 futures = "0.3.25"
 shared-memory-server = { workspace = true }
diff --git a/binaries/daemon/src/spawn.rs b/binaries/daemon/src/spawn.rs
index cf6a3092..7d75b755 100644
--- a/binaries/daemon/src/spawn.rs
+++ b/binaries/daemon/src/spawn.rs
@@ -89,7 +89,8 @@ impl Spawner {
             node_id: node_id.clone(),
             run_config: node.kind.run_config(),
             daemon_communication,
-            dataflow_descriptor: self.dataflow_descriptor.clone(),
+            dataflow_descriptor: serde_yaml::to_value(&self.dataflow_descriptor)
+                .context("failed to serialize dataflow descriptor to YAML")?,
             dynamic: node.kind.dynamic(),
         };
 
diff --git a/binaries/runtime/Cargo.toml b/binaries/runtime/Cargo.toml
index 270ba264..73e6c615 100644
--- a/binaries/runtime/Cargo.toml
+++ b/binaries/runtime/Cargo.toml
@@ -21,7 +21,7 @@ eyre = "0.6.8"
 futures = "0.3.21"
 futures-concurrency = "7.1.0"
 libloading = "0.7.3"
-serde_yaml = "0.8.23"
+serde_yaml = { workspace = true }
 tokio = { version = "1.24.2", features = ["full"] }
 tokio-stream = "0.1.8"
 # pyo3-abi3 flag allow simpler linking. See: https://pyo3.rs/v0.13.2/building_and_distribution.html
diff --git a/binaries/runtime/src/lib.rs b/binaries/runtime/src/lib.rs
index ea949bf4..6b3311bc 100644
--- a/binaries/runtime/src/lib.rs
+++ b/binaries/runtime/src/lib.rs
@@ -43,7 +43,8 @@ pub fn main() -> eyre::Result<()> {
             .wrap_err("failed to set up tracing subscriber")?;
     }
 
-    let dataflow_descriptor = config.dataflow_descriptor.clone();
+    let dataflow_descriptor = serde_yaml::from_value(config.dataflow_descriptor.clone())
+        .context("failed to parse dataflow descriptor")?;
 
     let operator_definition = if operators.is_empty() {
         bail!("no operators");
diff --git a/libraries/core/Cargo.toml b/libraries/core/Cargo.toml
index af467ffe..d50765ef 100644
--- a/libraries/core/Cargo.toml
+++ b/libraries/core/Cargo.toml
@@ -13,7 +13,7 @@ repository.workspace = true
 dora-message = { workspace = true }
 eyre = "0.6.8"
 serde = { version = "1.0.136", features = ["derive"] }
-serde_yaml = "0.9.11"
+serde_yaml = { workspace = true }
 once_cell = "1.13.0"
 which = "5.0.0"
 uuid = { version = "1.7", features = ["serde", "v7"] }
diff --git a/libraries/message/Cargo.toml b/libraries/message/Cargo.toml
index 7bb3f673..7e4e179f 100644
--- a/libraries/message/Cargo.toml
+++ b/libraries/message/Cargo.toml
@@ -23,7 +23,7 @@ aligned-vec = { version = "0.5.0", features = ["serde"] }
 semver = { version = "1.0.23", features = ["serde"] }
 schemars = "0.8.19"
 uhlc = "0.5.1"
-serde_yaml = "0.9.11"
+serde_yaml = { workspace = true }
 once_cell = "1.13.0"
 serde-with-expand-env = "1.1.0"
 bincode = "1.3.3"
diff --git a/libraries/message/src/daemon_to_node.rs b/libraries/message/src/daemon_to_node.rs
index acc1630e..e0ce466c 100644
--- a/libraries/message/src/daemon_to_node.rs
+++ b/libraries/message/src/daemon_to_node.rs
@@ -23,7 +23,7 @@ pub struct NodeConfig {
     pub node_id: NodeId,
     pub run_config: NodeRunConfig,
     pub daemon_communication: DaemonCommunication,
-    pub dataflow_descriptor: Descriptor,
+    pub dataflow_descriptor: serde_yaml::Value,
     pub dynamic: bool,
 }