diff --git a/aya-gen/src/generate.rs b/aya-gen/src/generate.rs
index 12ac7034..4bd4b8e7 100644
--- a/aya-gen/src/generate.rs
+++ b/aya-gen/src/generate.rs
@@ -43,7 +43,21 @@ pub fn generate<T: AsRef<str>>(
     types: &[T],
     additional_flags: &[T],
 ) -> Result<String, Error> {
+    let additional_flags = additional_flags
+        .iter()
+        .map(|s| s.as_ref().into())
+        .collect::<Vec<_>>();
+
     let mut bindgen = bindgen::bpf_builder();
+    let (additional_flags, ctypes_prefix) = extract_ctypes_prefix(&additional_flags);
+
+    if let Some(prefix) = ctypes_prefix {
+        bindgen = bindgen.ctypes_prefix(prefix)
+    }
+
+    for ty in types {
+        bindgen = bindgen.allowlist_type(ty);
+    }
 
     let (c_header, name) = match &input_file {
         InputFile::Btf(path) => (c_header_from_btf(path)?, "kernel_types.h"),
@@ -53,22 +67,12 @@ pub fn generate<T: AsRef<str>>(
         ),
     };
 
-    for ty in types {
-        bindgen = bindgen.allowlist_type(ty);
-    }
-
     let dir = tempdir().unwrap();
     let file_path = dir.path().join(name);
     let mut file = File::create(&file_path).unwrap();
     let _ = file.write(c_header.as_bytes()).unwrap();
 
-    let flags = combine_flags(
-        &bindgen.command_line_flags(),
-        &additional_flags
-            .iter()
-            .map(|s| s.as_ref().into())
-            .collect::<Vec<_>>(),
-    );
+    let flags = combine_flags(&bindgen.command_line_flags(), &additional_flags);
 
     let output = Command::new("bindgen")
         .arg(file_path)
@@ -104,14 +108,28 @@ fn c_header_from_btf(path: &Path) -> Result<String, Error> {
     Ok(str::from_utf8(&output.stdout).unwrap().to_owned())
 }
 
+fn extract_ctypes_prefix(s: &[String]) -> (Vec<String>, Option<String>) {
+    if let Some(index) = s.iter().position(|el| el == "--ctypes-prefix") {
+        if index < s.len() - 1 {
+            let mut flags = Vec::new();
+            flags.extend_from_slice(&s[0..index]);
+            // skip ["--ctypes-prefix", "value"]
+            flags.extend_from_slice(&s[index + 2..]);
+            return (flags, s.get(index + 1).cloned());
+        }
+    }
+
+    (s.to_vec(), None)
+}
+
 fn combine_flags(s1: &[String], s2: &[String]) -> Vec<String> {
-    let mut args = Vec::new();
+    let mut flags = Vec::new();
     let mut extra = Vec::new();
 
     for s in [s1, s2] {
         let mut s = s.splitn(2, |el| el == "--");
         // append args
-        args.extend(s.next().unwrap().iter().cloned());
+        flags.extend(s.next().unwrap().iter().cloned());
         if let Some(e) = s.next() {
             // append extra args
             extra.extend(e.iter().cloned());
@@ -120,23 +138,47 @@ fn combine_flags(s1: &[String], s2: &[String]) -> Vec<String> {
 
     // append extra args
     if !extra.is_empty() {
-        args.push("--".to_string());
-        args.extend(extra);
+        flags.push("--".to_string());
+        flags.extend(extra);
     }
 
-    args
+    flags
 }
 
 #[cfg(test)]
 mod test {
-    use super::combine_flags;
+    use super::{combine_flags, extract_ctypes_prefix};
 
     fn to_vec(s: &str) -> Vec<String> {
         s.split(" ").map(|x| x.into()).collect()
     }
 
     #[test]
-    fn combine_arguments_test() {
+    fn test_extract_ctypes_prefix() {
+        let (flags, prefix) = extract_ctypes_prefix(&to_vec("foo --ctypes-prefix bar baz"));
+        assert_eq!(flags, to_vec("foo baz"));
+        assert_eq!(prefix, Some("bar".to_string()));
+
+        let (flags, prefix) = extract_ctypes_prefix(&to_vec("foo --ctypes-prefi bar baz"));
+        assert_eq!(flags, to_vec("foo --ctypes-prefi bar baz"));
+        assert_eq!(prefix, None);
+
+        let (flags, prefix) = extract_ctypes_prefix(&to_vec("--foo bar --ctypes-prefix"));
+        assert_eq!(flags, to_vec("--foo bar --ctypes-prefix"));
+        assert_eq!(prefix, None);
+
+        let (flags, prefix) = extract_ctypes_prefix(&to_vec("--ctypes-prefix foo"));
+        let empty: Vec<String> = Vec::new();
+        assert_eq!(flags, empty);
+        assert_eq!(prefix, Some("foo".to_string()));
+
+        let (flags, prefix) = extract_ctypes_prefix(&to_vec("--ctypes-prefix"));
+        assert_eq!(flags, to_vec("--ctypes-prefix"));
+        assert_eq!(prefix, None);
+    }
+
+    #[test]
+    fn test_combine_flags() {
         assert_eq!(
             combine_flags(&to_vec("a b"), &to_vec("c d"),).join(" "),
             "a b c d".to_string(),