diff --git a/src/bin/cargo/commands/vendor.rs b/src/bin/cargo/commands/vendor.rs
index 96b30676732..63db209cca4 100644
--- a/src/bin/cargo/commands/vendor.rs
+++ b/src/bin/cargo/commands/vendor.rs
@@ -60,7 +60,8 @@ pub fn exec(gctx: &mut GlobalContext, args: &ArgMatches) -> CliResult {
     // to respect any of the `source` configuration in Cargo itself. That's
     // intended for other consumers of Cargo, but we want to go straight to the
     // source, e.g. crates.io, to fetch crates.
-    if !args.flag("respect-source-config") {
+    let respect_source_config = args.flag("respect-source-config");
+    if !respect_source_config {
         gctx.values_mut()?.remove("source");
     }
 
@@ -80,6 +81,7 @@ pub fn exec(gctx: &mut GlobalContext, args: &ArgMatches) -> CliResult {
                 .unwrap_or_default()
                 .cloned()
                 .collect(),
+            respect_source_config,
         },
     )?;
     Ok(())
diff --git a/src/cargo/ops/vendor.rs b/src/cargo/ops/vendor.rs
index 44e2a2addd2..381e2528a43 100644
--- a/src/cargo/ops/vendor.rs
+++ b/src/cargo/ops/vendor.rs
@@ -1,8 +1,10 @@
 use crate::core::shell::Verbosity;
+use crate::core::SourceId;
 use crate::core::{GitReference, Package, Workspace};
 use crate::ops;
 use crate::sources::path::PathSource;
 use crate::sources::PathEntry;
+use crate::sources::SourceConfigMap;
 use crate::sources::CRATES_IO_REGISTRY;
 use crate::util::cache_lock::CacheLockMode;
 use crate::util::{try_canonicalize, CargoResult, GlobalContext};
@@ -21,6 +23,7 @@ pub struct VendorOptions<'a> {
     pub versioned_dirs: bool,
     pub destination: &'a Path,
     pub extra: Vec<PathBuf>,
+    pub respect_source_config: bool,
 }
 
 pub fn vendor(ws: &Workspace<'_>, opts: &VendorOptions<'_>) -> CargoResult<()> {
@@ -76,6 +79,32 @@ enum VendorSource {
     },
 }
 
+/// Cache for mapping replaced sources to replacements.
+struct SourceReplacementCache<'gctx> {
+    map: SourceConfigMap<'gctx>,
+    cache: HashMap<SourceId, SourceId>,
+}
+
+impl SourceReplacementCache<'_> {
+    fn new(gctx: &GlobalContext) -> CargoResult<SourceReplacementCache<'_>> {
+        Ok(SourceReplacementCache {
+            map: SourceConfigMap::new(gctx)?,
+            cache: Default::default(),
+        })
+    }
+
+    fn get(&mut self, id: SourceId) -> CargoResult<SourceId> {
+        use std::collections::hash_map::Entry;
+        match self.cache.entry(id) {
+            Entry::Occupied(e) => Ok(e.get().clone()),
+            Entry::Vacant(e) => {
+                let replaced = self.map.load(id, &HashSet::new())?.replaced_source_id();
+                Ok(e.insert(replaced).clone())
+            }
+        }
+    }
+}
+
 fn sync(
     gctx: &GlobalContext,
     workspaces: &[&Workspace<'_>],
@@ -101,6 +130,8 @@ fn sync(
         }
     }
 
+    let mut source_replacement_cache = SourceReplacementCache::new(gctx)?;
+
     // First up attempt to work around rust-lang/cargo#5956. Apparently build
     // artifacts sprout up in Cargo's global cache for whatever reason, although
     // it's unsure what tool is causing these issues at this time. For now we
@@ -121,20 +152,31 @@ fn sync(
             .context("failed to download packages")?;
 
         for pkg in resolve.iter() {
+            let sid = if opts.respect_source_config {
+                source_replacement_cache.get(pkg.source_id())?
+            } else {
+                pkg.source_id()
+            };
+
             // Don't delete actual source code!
-            if pkg.source_id().is_path() {
-                if let Ok(path) = pkg.source_id().url().to_file_path() {
+            if sid.is_path() {
+                if let Ok(path) = sid.url().to_file_path() {
                     if let Ok(path) = try_canonicalize(path) {
                         to_remove.remove(&path);
                     }
                 }
                 continue;
             }
-            if pkg.source_id().is_git() {
+            if sid.is_git() {
                 continue;
             }
-            if let Ok(pkg) = packages.get_one(pkg) {
-                drop(fs::remove_dir_all(pkg.root()));
+
+            // Only delete sources that are safe to delete, i.e. they are caches.
+            if sid.is_registry() {
+                if let Ok(pkg) = packages.get_one(pkg) {
+                    drop(fs::remove_dir_all(pkg.root()));
+                }
+                continue;
             }
         }
     }
diff --git a/tests/testsuite/vendor.rs b/tests/testsuite/vendor.rs
index 7ea31b5b5d9..dbf956eedf4 100644
--- a/tests/testsuite/vendor.rs
+++ b/tests/testsuite/vendor.rs
@@ -1939,3 +1939,45 @@ fn vendor_crate_with_ws_inherit() {
 "#]])
         .run();
 }
+
+#[cargo_test]
+fn dont_delete_non_registry_sources_with_respect_source_config() {
+    let p = project()
+        .file(
+            "Cargo.toml",
+            r#"
+                [package]
+                name = "foo"
+                version = "0.1.0"
+
+                [dependencies]
+                log = "0.3.5"
+            "#,
+        )
+        .file("src/lib.rs", "")
+        .build();
+
+    Package::new("log", "0.3.5").publish();
+
+    p.cargo("vendor --respect-source-config").run();
+    let lock = p.read_file("vendor/log/Cargo.toml");
+    assert!(lock.contains("version = \"0.3.5\""));
+
+    add_crates_io_vendor_config(&p);
+    p.cargo("vendor --respect-source-config new-vendor-dir")
+        .with_stderr_data(str![[r#"
+   Vendoring log v0.3.5 ([ROOT]/foo/vendor/log) to new-vendor-dir/log
+To use vendored sources, add this to your .cargo/config.toml for this project:
+
+
+"#]])
+        .with_stdout_data(str![[r#"
+[source.crates-io]
+replace-with = "vendored-sources"
+
+[source.vendored-sources]
+directory = "new-vendor-dir"
+
+"#]])
+        .run();
+}