diff --git a/doc/manual/local.mk b/doc/manual/local.mk
index 2a32f1a63..fdcd131de 100644
--- a/doc/manual/local.mk
+++ b/doc/manual/local.mk
@@ -50,11 +50,14 @@ $(d)/src/SUMMARY.md: $(d)/src/SUMMARY.md.in $(d)/src/command-ref/new-cli
 
 $(d)/src/command-ref/new-cli: $(d)/nix.json $(d)/generate-manpage.nix $(bindir)/nix
 	@rm -rf $@
-	$(trace-gen) $(nix-eval) --write-to $@ --expr 'import doc/manual/generate-manpage.nix { toplevel = builtins.readFile $<; }'
+	$(trace-gen) $(nix-eval) --write-to $@.tmp --expr 'import doc/manual/generate-manpage.nix { toplevel = builtins.readFile $<; }'
+	$(trace-gen) sed -i $@.tmp/*.md -e 's^@docroot@^../..^g'
+	@mv $@.tmp $@
 
 $(d)/src/command-ref/conf-file.md: $(d)/conf-file.json $(d)/generate-options.nix $(d)/src/command-ref/conf-file-prefix.md $(bindir)/nix
 	@cat doc/manual/src/command-ref/conf-file-prefix.md > $@.tmp
-	$(trace-gen) $(nix-eval) --expr 'import doc/manual/generate-options.nix (builtins.fromJSON (builtins.readFile $<))' >> $@.tmp
+	$(trace-gen) $(nix-eval) --expr 'import doc/manual/generate-options.nix (builtins.fromJSON (builtins.readFile $<))' \
+	  | sed -e 's^@docroot@^..^g'>> $@.tmp
 	@mv $@.tmp $@
 
 $(d)/nix.json: $(bindir)/nix
@@ -67,7 +70,8 @@ $(d)/conf-file.json: $(bindir)/nix
 
 $(d)/src/language/builtins.md: $(d)/builtins.json $(d)/generate-builtins.nix $(d)/src/language/builtins-prefix.md $(bindir)/nix
 	@cat doc/manual/src/language/builtins-prefix.md > $@.tmp
-	$(trace-gen) $(nix-eval) --expr 'import doc/manual/generate-builtins.nix (builtins.fromJSON (builtins.readFile $<))' >> $@.tmp
+	$(trace-gen) $(nix-eval) --expr 'import doc/manual/generate-builtins.nix (builtins.fromJSON (builtins.readFile $<))' \
+	  | sed -e 's^@docroot@^..^g' >> $@.tmp
 	@cat doc/manual/src/language/builtins-suffix.md >> $@.tmp
 	@mv $@.tmp $@
 
diff --git a/src/libcmd/common-eval-args.cc b/src/libcmd/common-eval-args.cc
index 0e321e5e4..908127b4d 100644
--- a/src/libcmd/common-eval-args.cc
+++ b/src/libcmd/common-eval-args.cc
@@ -34,8 +34,8 @@ MixEvalArgs::MixEvalArgs()
         .shortName = 'I',
         .description = R"(
   Add *path* to the Nix search path. The Nix search path is
-  initialized from the colon-separated [`NIX_PATH`](./env-common.md#env-NIX_PATH) environment
-  variable, and is used to look up the location of Nix expressions using [paths](../language/values.md#type-path) enclosed in angle
+  initialized from the colon-separated [`NIX_PATH`](@docroot@/command-ref/env-common.md#env-NIX_PATH) environment
+  variable, and is used to look up the location of Nix expressions using [paths](@docroot@/language/values.md#type-path) enclosed in angle
   brackets (i.e., `<nixpkgs>`).
 
   For instance, passing
diff --git a/src/libexpr/primops.cc b/src/libexpr/primops.cc
index 9ef91cbc5..5519642b1 100644
--- a/src/libexpr/primops.cc
+++ b/src/libexpr/primops.cc
@@ -1917,7 +1917,7 @@ static RegisterPrimOp primop_toFile({
       ```
 
       Note that `${configFile}` is a
-      [string interpolation](language/values.md#type-string), so the result of the
+      [string interpolation](@docroot@/language/values.md#type-string), so the result of the
       expression `configFile`
       (i.e., a path like `/nix/store/m7p7jfny445k...-foo.conf`) will be
       spliced into the resulting string.
diff --git a/src/libstore/globals.hh b/src/libstore/globals.hh
index f026c8808..7111def92 100644
--- a/src/libstore/globals.hh
+++ b/src/libstore/globals.hh
@@ -676,7 +676,7 @@ public:
           - the store object is signed by one of the [`trusted-public-keys`](#conf-trusted-public-keys)
           - the substituter is in the [`trusted-substituters`](#conf-trusted-substituters) list
           - the [`require-sigs`](#conf-require-sigs) option has been set to `false`
-          - the store object is [output-addressed](glossary.md#gloss-output-addressed-store-object)
+          - the store object is [output-addressed](@docroot@/glossary.md#gloss-output-addressed-store-object)
         )",
         {"binary-caches"}};