diff --git a/Cargo.lock b/Cargo.lock
index 68a124b8b..3833e7bb9 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -26,6 +26,15 @@ dependencies = [
  "memchr",
 ]
 
+[[package]]
+name = "alloca"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e5a7d05ea6aea7e9e64d25b9156ba2fee3fdd659e34e41063cd2fc7cd020d7f4"
+dependencies = [
+ "cc",
+]
+
 [[package]]
 name = "android_system_properties"
 version = "0.1.5"
@@ -35,6 +44,12 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "anes"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299"
+
 [[package]]
 name = "anstream"
 version = "1.0.0"
@@ -186,6 +201,12 @@ version = "3.20.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "72f5acc6cb2ba439de613abc23857ec3d78374d8ed5ac84e9d11336e87da8649"
 
+[[package]]
+name = "cast"
+version = "0.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5"
+
 [[package]]
 name = "cc"
 version = "1.4.0"
@@ -226,11 +247,38 @@ dependencies = [
  "windows-link",
 ]
 
+[[package]]
+name = "ciborium"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "42e69ffd6f0917f5c029256a24d0161db17cea3997d185db0d35926308770f0e"
+dependencies = [
+ "ciborium-io",
+ "ciborium-ll",
+ "serde",
+]
+
+[[package]]
+name = "ciborium-io"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "05afea1e0a06c9be33d539b876f1ce3692f4afea2cb41f740e7743225ed1c757"
+
+[[package]]
+name = "ciborium-ll"
+version = "0.2.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "57663b653d948a338bfb3eeba9bb2fd5fcfaecb9e199e87e1eda4d9e8b240fd9"
+dependencies = [
+ "ciborium-io",
+ "half",
+]
+
 [[package]]
 name = "clang-sys"
-version = "1.8.1"
+version = "1.9.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b023947811758c97c59bf9d1c188fd619ad4718dcaa767947df1cadb14f39f4"
+checksum = "157a8ba7b480713b56f4c09fd13fc3e0a22a5dfab8097ba61cbc5feef950788a"
 dependencies = [
  "glob",
  "libc",
@@ -363,6 +411,72 @@ version = "0.8.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "773648b94d0e5d620f64f280777445740e61fe701025087ec8b57f45c791888b"
 
+[[package]]
+name = "criterion"
+version = "0.8.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "950046b2aa2492f9a536f5f4f9a3de7b9e2476e575e05bd6c333371add4d98f3"
+dependencies = [
+ "alloca",
+ "anes",
+ "cast",
+ "ciborium",
+ "clap",
+ "criterion-plot",
+ "itertools 0.13.0",
+ "num-traits",
+ "oorandom",
+ "page_size",
+ "plotters",
+ "rayon",
+ "regex",
+ "serde",
+ "serde_json",
+ "tinytemplate",
+ "walkdir",
+]
+
+[[package]]
+name = "criterion-plot"
+version = "0.8.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d8d80a2f4f5b554395e47b5d8305bc3d27813bacb73493eb1001e8f76dae29ea"
+dependencies = [
+ "cast",
+ "itertools 0.13.0",
+]
+
+[[package]]
+name = "crossbeam-deque"
+version = "0.8.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5181e0de7b61eb03a81e347d6dd8797bae9da5146707b51077e2d71a54ec0ceb"
+dependencies = [
+ "crossbeam-epoch",
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-epoch"
+version = "0.9.20"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2d6914041f254d6e9176c01941b21115dcfb7089e55135a35411081bd106ef3f"
+dependencies = [
+ "crossbeam-utils",
+]
+
+[[package]]
+name = "crossbeam-utils"
+version = "0.8.22"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "61803da095bee82a81bb1a452ecc25d3b2f1416d1897eb86430c6159ef717c17"
+
+[[package]]
+name = "crunchy"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "460fbee9c2c2f33933d720630a6a0bac33ba7053db5344fac858d4b8952d77d5"
+
 [[package]]
 name = "csv"
 version = "1.4.0"
@@ -623,6 +737,17 @@ version = "0.3.4"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e4eba85ea1d0a966a983acd07deee566e67395d2d96b6fb39e62b5a833f1eb0b"
 
+[[package]]
+name = "half"
+version = "2.7.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6ea2d84b969582b4b1864a92dc5d27cd2b77b622a8d79306834f1be5ba20d84b"
+dependencies = [
+ "cfg-if",
+ "crunchy",
+ "zerocopy",
+]
+
 [[package]]
 name = "hashbrown"
 version = "0.15.5"
@@ -936,6 +1061,7 @@ dependencies = [
  "clap-markdown",
  "colored 3.1.1",
  "context_manager",
+ "criterion",
  "csv",
  "derive_more",
  "dirs",
@@ -1033,6 +1159,12 @@ version = "1.70.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "384b8ab6d37215f3c5301a95a4accb5d64aa607f1fcb26a11b5303878451b4fe"
 
+[[package]]
+name = "oorandom"
+version = "11.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d6790f58c7ff633d8771f42965289203411a5e5c68388703c06e14f24770b41e"
+
 [[package]]
 name = "optfield"
 version = "0.4.0"
@@ -1059,6 +1191,16 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "page_size"
+version = "0.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "30d5b2194ed13191c1999ae0704b7839fb18384fa22e49b57eeaa97d79ce40da"
+dependencies = [
+ "libc",
+ "winapi",
+]
+
 [[package]]
 name = "petgraph"
 version = "0.8.3"
@@ -1135,6 +1277,34 @@ dependencies = [
  "windows-sys 0.59.0",
 ]
 
+[[package]]
+name = "plotters"
+version = "0.3.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5aeb6f403d7a4911efb1e33402027fc44f29b5bf6def3effcc22d7bb75f2b747"
+dependencies = [
+ "num-traits",
+ "plotters-backend",
+ "plotters-svg",
+ "wasm-bindgen",
+ "web-sys",
+]
+
+[[package]]
+name = "plotters-backend"
+version = "0.3.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "df42e13c12958a16b3f7f4386b9ab1f3e7933914ecea48da7139435263a4172a"
+
+[[package]]
+name = "plotters-svg"
+version = "0.3.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "51bae2ac328883f7acdfea3d66a7c35751187f870bc81f94563733a154d7a670"
+dependencies = [
+ "plotters-backend",
+]
+
 [[package]]
 name = "predicates"
 version = "3.1.4"
@@ -1205,6 +1375,26 @@ version = "6.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f8dcc9c7d52a811697d2151c701e0d08956f92b0e24136cf4cf27b57a6a0d9bf"
 
+[[package]]
+name = "rayon"
+version = "1.12.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "fb39b166781f92d482534ef4b4b1b2568f42613b53e5b6c160e24cfbfa30926d"
+dependencies = [
+ "either",
+ "rayon-core",
+]
+
+[[package]]
+name = "rayon-core"
+version = "1.13.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "22e18b0f0062d30d4230b2e85ff77fdfe4326feb054b9783a3460d8435c8ab91"
+dependencies = [
+ "crossbeam-deque",
+ "crossbeam-utils",
+]
+
 [[package]]
 name = "redox_users"
 version = "0.5.2"
@@ -1337,6 +1527,15 @@ version = "1.0.23"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9774ba4a74de5f7b1c1451ed6cd5285a32eddb5cccb8cc655a4e50009e06477f"
 
+[[package]]
+name = "same-file"
+version = "1.0.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502"
+dependencies = [
+ "winapi-util",
+]
+
 [[package]]
 name = "semver"
 version = "1.0.28"
@@ -1373,6 +1572,19 @@ dependencies = [
  "syn 3.0.3",
 ]
 
+[[package]]
+name = "serde_json"
+version = "1.0.151"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c841b55ecdae098c80dcae9cf767f6f8a0c2cdb3416bbef72181df4d0fe73f14"
+dependencies = [
+ "itoa",
+ "memchr",
+ "serde",
+ "serde_core",
+ "zmij",
+]
+
 [[package]]
 name = "serde_spanned"
 version = "1.1.1"
@@ -1517,6 +1729,16 @@ dependencies = [
  "syn 3.0.3",
 ]
 
+[[package]]
+name = "tinytemplate"
+version = "1.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "be4d6b5f19ff7664e8c98d03e2139cb510db9b0a60b55f8e8709b689d939b6bc"
+dependencies = [
+ "serde",
+ "serde_json",
+]
+
 [[package]]
 name = "toml"
 version = "1.1.4+spec-1.1.0"
@@ -1628,6 +1850,16 @@ dependencies = [
  "libc",
 ]
 
+[[package]]
+name = "walkdir"
+version = "2.5.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b"
+dependencies = [
+ "same-file",
+ "winapi-util",
+]
+
 [[package]]
 name = "wasi"
 version = "0.11.1+wasi-snapshot-preview1"
@@ -1679,6 +1911,16 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "web-sys"
+version = "0.3.103"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8622dcb61c0bcc9fffa6938bed81210af2da9a7e4a1a834b2e37a59b6dfb6141"
+dependencies = [
+ "js-sys",
+ "wasm-bindgen",
+]
+
 [[package]]
 name = "which"
 version = "4.4.2"
@@ -1707,6 +1949,15 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
 
+[[package]]
+name = "winapi-util"
+version = "0.1.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c2a7b1c03c876122aa43f3020e6c3c3ee5c05081c9a00739faf7503aeba10d22"
+dependencies = [
+ "windows-sys 0.61.2",
+]
+
 [[package]]
 name = "winapi-x86_64-pc-windows-gnu"
 version = "0.4.0"
@@ -1923,3 +2174,29 @@ dependencies = [
  "arraydeque",
  "hashlink",
 ]
+
+[[package]]
+name = "zerocopy"
+version = "0.8.55"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b5a105cd7b140f6eeec8acff2ea38135d3cab283ada58540f629fe51e46696eb"
+dependencies = [
+ "zerocopy-derive",
+]
+
+[[package]]
+name = "zerocopy-derive"
+version = "0.8.55"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0fe976fb70c78cd64cccfe3a6fc142244e8a77b70959b30faf9d0ac37ee228eb"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.119",
+]
+
+[[package]]
+name = "zmij"
+version = "1.0.23"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "29666d0abbfad1e3dc4dcf6144730dd3a3ab225bbbdac83319345b1b44ccfc1b"
diff --git a/Cargo.toml b/Cargo.toml
index f76e169ed..f7c2b73f5 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -48,6 +48,7 @@ context_manager = "0.1.3"
 [dev-dependencies]
 assert_cmd = "2.2.2"
 colored = "3.0.0"
+criterion = "0.8.2"
 logtest = "2.0.0"
 map-macro = "0.3.0"
 ordered-float = "5.1.0"
@@ -85,3 +86,10 @@ implicit_hasher = "allow"
 cast_lossless = "allow"
 return_self_not_must_use = "allow"
 from_iter_instead_of_collect = "allow"
+
+[[bench]]
+name = "examples"
+harness = false
+
+[features]
+bench = []
diff --git a/benches/examples.rs b/benches/examples.rs
new file mode 100644
index 000000000..4762fb6b8
--- /dev/null
+++ b/benches/examples.rs
@@ -0,0 +1,35 @@
+use criterion::{Criterion, criterion_group, criterion_main};
+use muse2::cli::RunOpts;
+use muse2::cli::example::handle_example_run_command;
+use muse2::example::get_example_names;
+use std::hint::black_box;
+
+/// Benchmark the example run command for all examples
+fn criterion_benchmark(c: &mut Criterion) {
+    let example_names = get_example_names();
+    let output_root = tempfile::TempDir::new()
+        .expect("Failed to create temporary output directory for benchmarks");
+    let output_dir = output_root.path().join("muse2-example-bench-output");
+    let options = RunOpts {
+        output_dir: Some(output_dir),
+        overwrite: true,
+        debug_model: false,
+        no_copy_input_files: false,
+    };
+    let mut group = c.benchmark_group("example_run");
+    group
+        .noise_threshold(0.05) // Set a noise threshold of 5%
+        .sample_size(20); // Set the sample size to 20 iterations
+
+    for name in example_names {
+        group.bench_function(format!("{name} example"), |b| {
+            b.iter(|| {
+                handle_example_run_command(black_box(name), black_box(false), black_box(&options))
+                    .unwrap_or(());
+            });
+        });
+    }
+}
+
+criterion_group!(benches, criterion_benchmark);
+criterion_main!(benches);
diff --git a/docs/developer_guide/coding.md b/docs/developer_guide/coding.md
index 4496219be..bb55ac0b2 100644
--- a/docs/developer_guide/coding.md
+++ b/docs/developer_guide/coding.md
@@ -74,3 +74,57 @@ just coverage --open
 
 This will generate a report in HTML format showing which lines are not currently covered by tests
 and open it in your default browser.
+
+## Working with the benchmarking framework
+
+MUSE2 includes a benchmarking framework to measure the performance of various components using the
+[Criterion.rs] library. To run all the available benchmarks, use the following command:
+
+```sh
+cargo bench --features bench
+```
+
+The `--features bench` flag disables some aspects of the code that are incompatible with the
+benchmarking, like singleton objects that can be only instantiated once and throw an error otherwise.
+See `rust` documentation for more information about [features].
+
+You can also run specific benchmarks by specifying their names:
+
+```sh
+cargo bench --features bench --bench <benchmark_name>
+```
+
+For example, to run the `examples` benchmark, you would use:
+
+```sh
+cargo bench --features bench --bench examples
+```
+
+If run more than once, the benchmarking framework will compare the results of the current run with the
+previous run and report the differences. This is useful for checking whether a change has
+introduced a performance regression.
+
+[Criterion.rs] automatically generates an HTML report that can be found in the
+`target/criterion/report` directory. You can open it with your web browser to see the results and
+navigate through the different benchmarks.
+
+### Adding new benchmarks
+
+To add a new benchmark, i.e. a collection of related performance tests, create a new file in the
+`benches` directory with the name of your benchmark. For example, to add a benchmark for the `foo`
+functionality, you would create a file called `benches/foo.rs`. Then `foo` will need to be added to
+`cargo.toml` under the `[bench]` section, like so:
+
+```toml
+[[bench]]
+name = "foo"
+harness = false
+```
+
+The `harness = false` line is necessary because Criterion.rs provides its own test harness, which
+is incompatible with the default Rust test harness. Within the new benchmark file, you can then add
+your performance tests using the Criterion.rs API. Check `benches/examples.rs` for an example of how
+to do this. More information about writing benchmarks can be found in the [Criterion.rs] documentation.
+
+[Criterion.rs]: https://bheisler.github.io/criterion.rs/book/index.html
+[features]: https://doc.rust-lang.org/cargo/reference/features.html
diff --git a/src/cli.rs b/src/cli.rs
index 416b602fc..67f1645a8 100644
--- a/src/cli.rs
+++ b/src/cli.rs
@@ -182,8 +182,11 @@ pub fn handle_run_command(model_path: &Path, opts: &RunOpts) -> Result<()> {
             .context("Failed to copy input files to output directory.")?;
     }
     // Initialise program logger
-    log::init(&settings.log_level, Some(output_path)).context("Failed to initialise logging.")?;
-
+    if !cfg!(feature = "bench") {
+        // Don't initialise logging when running bench, as it will interfere with the process
+        log::init(&settings.log_level, Some(output_path))
+            .context("Failed to initialise logging.")?;
+    }
     info!("Starting MUSE2 v{}", env!("CARGO_PKG_VERSION"));
 
     // Load the model to run
diff --git a/src/model/parameters.rs b/src/model/parameters.rs
index ef542d3cb..284a913d7 100644
--- a/src/model/parameters.rs
+++ b/src/model/parameters.rs
@@ -53,7 +53,7 @@ pub fn dangerous_model_options_enabled() -> bool {
 fn set_dangerous_model_options_flag(enabled: bool) {
     let result = DANGEROUS_OPTIONS_ENABLED.set(enabled);
     if result.is_err() {
-        if cfg!(test) {
+        if cfg!(test) || cfg!(feature = "bench") {
             // Sanity check
             assert_eq!(enabled, dangerous_model_options_enabled());
         } else {