diff --git a/Cargo.toml b/Cargo.toml
index 7f924ac..70ca4be 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -9,6 +9,7 @@ edition = "2021"
 
 [dependencies]
 anyhow = "1.0.71"
+base64 = "0.21.2"
 bzip2 = "0.4.4"
 clap = { version = "4.2.5", features = ["derive"] }
 directories = "5.0.0"
@@ -23,9 +24,10 @@ zip = { version = "0.6.4", features = ["deflate"] }
 zstd = "0.12.3"
 
 [build-dependencies]
-rand = "0.8.5"
+base64 = "0.21.2"
 flate2 = "1.0.26"
 highway = "1.0.0"
+rand = "0.8.5"
 regex = "1.8.1"
 reqwest = { version = "0.11", features = ["blocking", "rustls-tls"], default-features = false }
 tar = "0.4.38"
diff --git a/build.rs b/build.rs
index 785fec5..f6d2f76 100644
--- a/build.rs
+++ b/build.rs
@@ -5,6 +5,7 @@ use std::hash::{Hash, Hasher};
 use std::io::Read;
 use std::path::PathBuf;
 
+use base64::{engine::general_purpose::STANDARD_NO_PAD, Engine as _};
 use highway::PortableHash;
 use rand::distributions::{Alphanumeric, DistString};
 use regex::Regex;
@@ -349,10 +350,12 @@ fn set_project_dependency_file(dependency_file: &str) {
     }
 
     let file_name = path.file_name().unwrap().to_str().unwrap();
+    let contents = fs::read_to_string(dependency_file)
+        .unwrap_or_else(|_| panic!("\n\nFailed to read dependency file {dependency_file}\n\n"));
+
     set_runtime_variable(
         "PYAPP_PROJECT_DEPENDENCY_FILE",
-        fs::read_to_string(dependency_file)
-            .unwrap_or_else(|_| panic!("\n\nFailed to read dependency file {dependency_file}\n\n")),
+        STANDARD_NO_PAD.encode(contents.as_bytes()),
     );
     set_runtime_variable("PYAPP__PROJECT_DEPENDENCY_FILE_NAME", file_name);
 }
diff --git a/docs/changelog.md b/docs/changelog.md
index 6e2b716..009e6ba 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -8,6 +8,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
 ## Unreleased
 
+***Fixed:***
+
+- Properly handle cases where options contain line feed characters
+
 ## 0.9.0 - 2023-06-21
 
 ***Changed:***
diff --git a/src/app.rs b/src/app.rs
index 0eef33e..dcadec7 100644
--- a/src/app.rs
+++ b/src/app.rs
@@ -2,6 +2,7 @@ use std::env;
 use std::path::{Path, PathBuf};
 
 use anyhow::{Context, Result};
+use base64::{engine::general_purpose::STANDARD_NO_PAD, Engine as _};
 use directories::ProjectDirs;
 use once_cell::sync::OnceCell;
 
@@ -23,6 +24,15 @@ pub fn initialize() -> Result<()> {
     Ok(())
 }
 
+fn decode_option(encoded: &'static str) -> String {
+    String::from_utf8(
+        STANDARD_NO_PAD
+            .decode(encoded)
+            .unwrap_or_else(|_| panic!("{} is not valid base64", encoded)),
+    )
+    .unwrap_or_else(|_| panic!("{} is not valid UTF-8", encoded))
+}
+
 pub fn embedded_distribution() -> &'static [u8] {
     // If this is empty, then the distribution will be downloaded at runtime
     include_bytes!("embed/distribution")
@@ -78,7 +88,7 @@ pub fn project_version() -> String {
 }
 
 pub fn project_dependency_file() -> String {
-    env!("PYAPP_PROJECT_DEPENDENCY_FILE").into()
+    decode_option(env!("PYAPP_PROJECT_DEPENDENCY_FILE"))
 }
 
 pub fn project_dependency_file_name() -> String {
@@ -94,7 +104,7 @@ pub fn exec_module() -> String {
 }
 
 pub fn exec_code() -> String {
-    env!("PYAPP_EXEC_CODE").into()
+    decode_option(env!("PYAPP_EXEC_CODE"))
 }
 
 pub fn pip_extra_args() -> String {