diff --git a/doc/manual/rl-next/cached-substituted-inputs.md b/doc/manual/rl-next/cached-substituted-inputs.md
new file mode 100644
index 000000000..b0b53a213
--- /dev/null
+++ b/doc/manual/rl-next/cached-substituted-inputs.md
@@ -0,0 +1,10 @@
+---
+synopsis: "Substituted flake inputs are no longer re-copied to the store"
+prs: [14041]
+---
+
+Since 2.25, Nix would fail to store a cache entry for substituted flake inputs,
+which in turn would cause them to be re-copied to the store on initial
+evaluation. Caching these inputs results in a near doubling of a performance in
+some cases — especially on I/O-bound machines and when using commands that
+fetch many inputs, like `nix flake archive/prefetch-inputs`
diff --git a/src/libfetchers/fetchers.cc b/src/libfetchers/fetchers.cc
index d40e97aa9..045aafdcb 100644
--- a/src/libfetchers/fetchers.cc
+++ b/src/libfetchers/fetchers.cc
@@ -4,6 +4,7 @@
 #include "nix/fetchers/fetch-to-store.hh"
 #include "nix/util/json-utils.hh"
 #include "nix/fetchers/fetch-settings.hh"
+#include "nix/fetchers/fetch-to-store.hh"
 
 #include <nlohmann/json.hpp>
 
@@ -336,6 +337,15 @@ std::pair<ref<SourceAccessor>, Input> Input::getAccessorUnchecked(ref<Store> sto
 
             accessor->fingerprint = getFingerprint(store);
 
+            // Store a cache entry for the substituted tree so later fetches
+            // can reuse the existing nar instead of copying the unpacked
+            // input back into the store on every evaluation.
+            if (accessor->fingerprint) {
+                ContentAddressMethod method = ContentAddressMethod::Raw::NixArchive;
+                auto cacheKey = makeFetchToStoreCacheKey(getName(), *accessor->fingerprint, method, "/");
+                settings->getCache()->upsert(cacheKey, *store, {}, storePath);
+            }
+
             accessor->setPathDisplay("«" + to_string() + "»");
 
             return {accessor, *this};