diff --git a/crates/ark/src/modules/positron/errors.R b/crates/ark/src/modules/positron/errors.R
index 99b2fb023a..b3e6d69a5f 100644
--- a/crates/ark/src/modules/positron/errors.R
+++ b/crates/ark/src/modules/positron/errors.R
@@ -129,6 +129,17 @@ globalInterruptHandler <- function(cnd) {
     format_traceback(traceback)
 }
 
+# Sources `file` with ark's global condition handlers re-registered.
+# Intended to be called from a `top_level_exec()` context (which clears the
+# handler stack), so that `globalCallingHandlers()` succeeds. This restores
+# message/error/warning rendering to match interactive behavior during
+# `.Rprofile` sourcing without putting calling-handlers on the stack that
+# would block user `globalCallingHandlers()` calls.
+.ps.errors.source_with_handlers <- function(file) {
+    initialize_errors()
+    sys.source(file, envir = globalenv())
+}
+
 # If a sink is active (either on output or on messages) messages
 # are always streamed to `stderr`. This follows rlang behaviour
 # and ensures messages can be sinked from stderr consistently.
@@ -278,10 +289,21 @@ initialize_errors <- function() {
     # Unregister all handlers and hold onto them
     handlers <- globalCallingHandlers(NULL)
 
+    existing_ps_handler <- vapply(
+        handlers,
+        function(h) {
+            isTRUE(all.equal(h, .ps.errors.globalErrorHandler)) ||
+                isTRUE(all.equal(h, .ps.errors.globalWarningHandler)) ||
+                isTRUE(all.equal(h, .ps.errors.globalMessageHandler)) ||
+                isTRUE(all.equal(h, globalInterruptHandler))
+        },
+        logical(1)
+    )
+
     # Inject our global error handler at the end.
     # This allows other existing error handlers to run ahead of us.
     handlers <- c(
-        handlers,
+        handlers[!existing_ps_handler],
         list(
             error = .ps.errors.globalErrorHandler,
             warning = .ps.errors.globalWarningHandler,
diff --git a/crates/ark/src/startup.rs b/crates/ark/src/startup.rs
index 291ef3833d..835c3508fb 100644
--- a/crates/ark/src/startup.rs
+++ b/crates/ark/src/startup.rs
@@ -12,7 +12,6 @@ use std::str::FromStr;
 use amalthea::socket::iopub::IOPubMessage;
 use amalthea::wire::stream::Stream;
 use amalthea::wire::stream::StreamOutput;
-use harp::environment::R_ENVS;
 use harp::exec::RFunction;
 use harp::exec::RFunctionExt;
 use libr::Rf_eval;
@@ -73,14 +72,16 @@ fn source_r_profile(path: &Path) {
     // `globalCallingHandlers()` from being called within `.Rprofile`s (can't
     // call it when there are handlers on the stack). That is a common place to
     // register global calling handlers, including in Gabor's prompt package.
-    // Source in the global env to mimic R.
+    // Source in the global env to mimic R. We do still register our handlers
+    // using globalCallingHandlers so that messages, warnings and errors appear
+    // as expected
+    let positron_ns = crate::modules::ARK_ENVS.positron_ns;
     let result = unsafe {
-        let call = RFunction::new("base", "sys.source")
+        let call = RFunction::from(".ps.errors.source_with_handlers")
             .param("file", path)
-            .param("envir", R_ENVS.global)
             .call
             .build();
-        harp::top_level_exec(|| Rf_eval(call.sexp, R_ENVS.global))
+        harp::top_level_exec(|| Rf_eval(call.sexp, positron_ns))
     };
 
     let Err(err) = result else {