diff --git a/crates/flake8_to_ruff/src/converter.rs b/crates/flake8_to_ruff/src/converter.rs
index 63a5c9dfd7..650e055125 100644
--- a/crates/flake8_to_ruff/src/converter.rs
+++ b/crates/flake8_to_ruff/src/converter.rs
@@ -16,36 +16,38 @@ pub fn convert(config: HashMap<String, HashMap<String, Option<String>>>) -> Resu
     // Parse each supported option.
     let mut options: Options = Default::default();
     for (key, value) in flake8 {
-        match key.as_str() {
-            "line-length" | "line_length" => match value.clone().unwrap().parse::<usize>() {
-                Ok(line_length) => options.line_length = Some(line_length),
-                Err(e) => eprintln!("Unable to parse '{key}' property: {e}"),
-            },
-            "select" => {
-                options.select = Some(parser::parse_prefix_codes(value.as_ref().unwrap()));
-            }
-            "extend-select" | "extend_select" => {
-                options.extend_select = parser::parse_prefix_codes(value.as_ref().unwrap());
-            }
-            "ignore" => {
-                options.ignore = parser::parse_prefix_codes(value.as_ref().unwrap());
-            }
-            "extend-ignore" | "extend_ignore" => {
-                options.extend_ignore = parser::parse_prefix_codes(value.as_ref().unwrap());
-            }
-            "exclude" => {
-                options.exclude = Some(parser::parse_strings(value.as_ref().unwrap()));
-            }
-            "extend-exclude" | "extend_exclude" => {
-                options.extend_exclude = parser::parse_strings(value.as_ref().unwrap());
-            }
-            "per-file-ignores" | "per_file_ignores" => {
-                match parser::parse_files_to_codes_mapping(value.as_ref().unwrap()) {
-                    Ok(per_file_ignores) => options.per_file_ignores = per_file_ignores,
+        if let Some(value) = value {
+            match key.as_str() {
+                "line-length" | "line_length" => match value.clone().parse::<usize>() {
+                    Ok(line_length) => options.line_length = Some(line_length),
                     Err(e) => eprintln!("Unable to parse '{key}' property: {e}"),
+                },
+                "select" => {
+                    options.select = Some(parser::parse_prefix_codes(value.as_ref()));
                 }
+                "extend-select" | "extend_select" => {
+                    options.extend_select = Some(parser::parse_prefix_codes(value.as_ref()));
+                }
+                "ignore" => {
+                    options.ignore = Some(parser::parse_prefix_codes(value.as_ref()));
+                }
+                "extend-ignore" | "extend_ignore" => {
+                    options.extend_ignore = Some(parser::parse_prefix_codes(value.as_ref()));
+                }
+                "exclude" => {
+                    options.exclude = Some(parser::parse_strings(value.as_ref()));
+                }
+                "extend-exclude" | "extend_exclude" => {
+                    options.extend_exclude = Some(parser::parse_strings(value.as_ref()));
+                }
+                "per-file-ignores" | "per_file_ignores" => {
+                    match parser::parse_files_to_codes_mapping(value.as_ref()) {
+                        Ok(per_file_ignores) => options.per_file_ignores = Some(per_file_ignores),
+                        Err(e) => eprintln!("Unable to parse '{key}' property: {e}"),
+                    }
+                }
+                _ => eprintln!("Skipping unsupported property: {key}"),
             }
-            _ => eprintln!("Skipping unsupported property: {key}"),
         }
     }
 
diff --git a/src/settings/configuration.rs b/src/settings/configuration.rs
index 273fa86867..3f280227cf 100644
--- a/src/settings/configuration.rs
+++ b/src/settings/configuration.rs
@@ -80,18 +80,20 @@ impl Configuration {
                 .unwrap_or_else(|| DEFAULT_EXCLUDE.clone()),
             extend_exclude: options
                 .extend_exclude
+                .unwrap_or_default()
                 .iter()
                 .map(|path| FilePattern::from_user(path, project_root))
                 .collect(),
-            extend_ignore: options.extend_ignore,
+            extend_ignore: options.extend_ignore.unwrap_or_default(),
             select: options
                 .select
                 .unwrap_or_else(|| vec![CheckCodePrefix::E, CheckCodePrefix::F]),
-            extend_select: options.extend_select,
-            ignore: options.ignore,
+            extend_select: options.extend_select.unwrap_or_default(),
+            ignore: options.ignore.unwrap_or_default(),
             line_length: options.line_length.unwrap_or(88),
             per_file_ignores: options
                 .per_file_ignores
+                .unwrap_or_default()
                 .into_iter()
                 .map(|pair| PerFileIgnore::new(pair, project_root))
                 .collect(),
diff --git a/src/settings/options.rs b/src/settings/options.rs
index bb00bfdc80..1ef93d8677 100644
--- a/src/settings/options.rs
+++ b/src/settings/options.rs
@@ -11,17 +11,12 @@ use crate::{flake8_quotes, pep8_naming};
 pub struct Options {
     pub line_length: Option<usize>,
     pub exclude: Option<Vec<String>>,
-    #[serde(default)]
-    pub extend_exclude: Vec<String>,
+    pub extend_exclude: Option<Vec<String>>,
     pub select: Option<Vec<CheckCodePrefix>>,
-    #[serde(default)]
-    pub extend_select: Vec<CheckCodePrefix>,
-    #[serde(default)]
-    pub ignore: Vec<CheckCodePrefix>,
-    #[serde(default)]
-    pub extend_ignore: Vec<CheckCodePrefix>,
-    #[serde(default)]
-    pub per_file_ignores: Vec<StrCheckCodePair>,
+    pub extend_select: Option<Vec<CheckCodePrefix>>,
+    pub ignore: Option<Vec<CheckCodePrefix>>,
+    pub extend_ignore: Option<Vec<CheckCodePrefix>>,
+    pub per_file_ignores: Option<Vec<StrCheckCodePair>>,
     pub dummy_variable_rgx: Option<String>,
     pub target_version: Option<PythonVersion>,
     // Plugins
diff --git a/src/settings/pyproject.rs b/src/settings/pyproject.rs
index 417e8f5bcb..cb8d172e9e 100644
--- a/src/settings/pyproject.rs
+++ b/src/settings/pyproject.rs
@@ -134,12 +134,12 @@ mod tests {
                 ruff: Some(Options {
                     line_length: None,
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -161,12 +161,12 @@ line-length = 79
                 ruff: Some(Options {
                     line_length: Some(79),
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -188,12 +188,12 @@ exclude = ["foo.py"]
                 ruff: Some(Options {
                     line_length: None,
                     exclude: Some(vec!["foo.py".to_string()]),
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -215,12 +215,12 @@ select = ["E501"]
                 ruff: Some(Options {
                     line_length: None,
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: Some(vec![CheckCodePrefix::E501]),
-                    extend_select: vec![],
-                    ignore: vec![],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: None,
+                    ignore: None,
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -243,12 +243,12 @@ ignore = ["E501"]
                 ruff: Some(Options {
                     line_length: None,
                     exclude: None,
-                    extend_exclude: vec![],
+                    extend_exclude: None,
                     select: None,
-                    extend_select: vec![CheckCodePrefix::M001],
-                    ignore: vec![CheckCodePrefix::E501],
-                    extend_ignore: vec![],
-                    per_file_ignores: vec![],
+                    extend_select: Some(vec![CheckCodePrefix::M001]),
+                    ignore: Some(vec![CheckCodePrefix::E501]),
+                    extend_ignore: None,
+                    per_file_ignores: None,
                     dummy_variable_rgx: None,
                     target_version: None,
                     flake8_quotes: None,
@@ -310,19 +310,19 @@ other-attribute = 1
             Options {
                 line_length: Some(88),
                 exclude: None,
-                extend_exclude: vec![
+                extend_exclude: Some(vec![
                     "excluded.py".to_string(),
                     "migrations".to_string(),
                     "directory/also_excluded.py".to_string(),
-                ],
+                ]),
                 select: None,
-                extend_select: vec![],
-                ignore: vec![],
-                extend_ignore: vec![],
-                per_file_ignores: vec![StrCheckCodePair {
+                extend_select: None,
+                ignore: None,
+                extend_ignore: None,
+                per_file_ignores: Some(vec![StrCheckCodePair {
                     pattern: "__init__.py".to_string(),
                     code: CheckCodePrefix::F401
-                }],
+                }]),
                 dummy_variable_rgx: None,
                 target_version: None,
                 flake8_quotes: Some(flake8_quotes::settings::Options {