diff --git a/eo-integration-tests/src/test/resources/org/eolang/snippets/auto-phi-with-application-precedence.yaml b/eo-integration-tests/src/test/resources/org/eolang/snippets/auto-phi-with-application-precedence.yaml
new file mode 100644
index 00000000000..63cfb302305
--- /dev/null
+++ b/eo-integration-tests/src/test/resources/org/eolang/snippets/auto-phi-with-application-precedence.yaml
@@ -0,0 +1,26 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+out: []
+file: org/eolang/snippets/foo.eo
+args: ["org.eolang.snippets.foo"]
+eo: |
+  +alias org.eolang.io.stdout
+  +alias org.eolang.txt.text
+  +alias org.eolang.structs.list
+  +package org.eolang.snippets
+
+  [] > foo
+    "abcdefghijk" > origin
+    origin > @
+    [cont-list] > custom-map
+      mapped. > @
+        cont-list
+        (text orgn).contains x >> [x]
+      origin > orgn!
+
+    [] +> test-custom-map
+      eq. > @
+        list (* true true)
+        foo.custom-map (list (* "abc" "ghi"))
diff --git a/eo-maven-plugin/src/test/resources/org/eolang/maven/transpile-packs/transpiles-auto-phi-formation-with-application-precedence.yaml b/eo-maven-plugin/src/test/resources/org/eolang/maven/transpile-packs/transpiles-auto-phi-formation-with-application-precedence.yaml
new file mode 100644
index 00000000000..81a783d1b05
--- /dev/null
+++ b/eo-maven-plugin/src/test/resources/org/eolang/maven/transpile-packs/transpiles-auto-phi-formation-with-application-precedence.yaml
@@ -0,0 +1,27 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+sheets:
+  - /org/eolang/maven/transpile/set-locators.xsl
+  - /org/eolang/maven/transpile/set-original-names.xsl
+  - /org/eolang/maven/transpile/classes.xsl
+  - /org/eolang/maven/transpile/tests.xsl
+  - /org/eolang/maven/transpile/attrs.xsl
+  - /org/eolang/maven/transpile/data.xsl
+  - /org/eolang/maven/transpile/to-java.xsl
+asserts:
+  - /object[not(errors)]
+  - //java[contains(text(), 'Φ.custom-map.ap🌵46.φ')]
+  - //java[contains(text(), 'Φ.custom-map.ap🌵46.φ.ρ.ρ.α0')]
+  - //java[contains(text(), 'Phi rrbb = Phi.Φ.take("org").take("eolang").take("text");')]
+  - //java[contains(text(), 'rrbb1 = new PhMethod(rrbb1, "orgn");')]
+  - //java[contains(text(), 'Phi rrb = new PhMethod(rrbb, "what");')]
+  - //java[contains(text(), 'Phi rrb1 = Phi.Φ.take("org").take("eolang").take("b");')]
+  - //java[contains(text(), 'Phi rr = new PhMethod(rrb, "ttt");')]
+input: |
+  [cont-list] > custom-map
+    mapped. > @
+      cont-list
+        ((text orgn).what b).ttt >> [y]
+    origin > orgn!
diff --git a/eo-parser/src/main/java/org/eolang/parser/XeEoListener.java b/eo-parser/src/main/java/org/eolang/parser/XeEoListener.java
index cffdb8963b8..7eaf5e8367e 100644
--- a/eo-parser/src/main/java/org/eolang/parser/XeEoListener.java
+++ b/eo-parser/src/main/java/org/eolang/parser/XeEoListener.java
@@ -10,6 +10,8 @@
 import java.util.Iterator;
 import java.util.List;
 import java.util.function.Supplier;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import org.antlr.v4.runtime.ParserRuleContext;
 import org.antlr.v4.runtime.Token;
@@ -35,6 +37,11 @@
     "PMD.GodClass"
 })
 final class XeEoListener implements EoListener, Iterable<Directive> {
+    /**
+     * Last application.
+     */
+    private static final Pattern LAST_APPLICATION = Pattern.compile("\\)\\.(\\p{L}[\\p{L}\\p{N}-]*)$");
+
     /**
      * Xembly directives we are building (mutable).
      */
@@ -158,7 +165,9 @@ public void exitObject(final EoParser.ObjectContext ctx) {
     @Override
     public void enterBound(final EoParser.BoundContext ctx) {
         if (ctx.just() != null && ctx.aphi() != null && ctx.just().finisher() != null) {
-            this.startAutoPhiFormation(ctx, ctx.just().finisher().getText());
+            this.startAutoPhiFormation(
+                ctx, XeEoListener.eoApplicationToXmir(ctx.just().finisher().getText())
+            );
         }
     }
 
@@ -367,7 +376,9 @@ public void exitHapplicationExtended(final EoParser.HapplicationExtendedContext
 
     @Override
     public void enterOnlyAphi(final EoParser.OnlyAphiContext ctx) {
-        this.startAutoPhiFormation(ctx, ctx.happlicationHeadExtended().getText());
+        this.startAutoPhiFormation(
+            ctx, XeEoListener.eoApplicationToXmir(ctx.happlicationHeadExtended().getText())
+        );
     }
 
     @Override
@@ -661,7 +672,12 @@ public void enterVapplicationArgUnbound(final EoParser.VapplicationArgUnboundCon
             final EoParser.VapplicationArgUnboundCurrentContext vertical =
                 ctx.vapplicationArgUnboundCurrent();
             if (vertical.just() != null || vertical.method() != null) {
-                this.startAutoPhiFormation(ctx, XeEoListener.verticalApplicationBase(vertical));
+                this.startAutoPhiFormation(
+                    ctx,
+                    XeEoListener.eoApplicationToXmir(
+                        XeEoListener.verticalApplicationBase(vertical)
+                    )
+                );
             }
         } else {
             this.objects.enter();
@@ -699,7 +715,7 @@ public void enterVapplicationArgUnboundNext(
     ) {
         if (ctx.aphi() != null) {
             this.startAutoPhiFormation(
-                ctx, ctx.vapplicationHead().getText()
+                ctx, XeEoListener.eoApplicationToXmir(ctx.vapplicationHead().getText())
             );
         }
     }
@@ -1210,13 +1226,44 @@ private String alphaAttr(final ParserRuleContext ctx, final String msg) {
      * @param application Application base
      */
     private void startAutoPhiFormation(final ParserRuleContext ctx, final String application) {
+        final Matcher matcher = XeEoListener.LAST_APPLICATION.matcher(application);
+        final String abase;
+        if (matcher.find()) {
+            abase = String.format(".%s", matcher.group(1));
+        } else {
+            abase = application;
+        }
         this.startAbstract(ctx)
             .enter().prop("name", new AutoName(ctx, "p").asString())
             .start(ctx)
-            .prop("base", String.format("ξ.ρ.%s", application))
+            .prop("base", abase)
             .prop("name", "φ");
     }
 
+    /**
+     * EO application to XMIR base.
+     * @param application Application to transform
+     * @return Application base in XMIR format
+     */
+    private static String eoApplicationToXmir(final String application) {
+        final String transformed = application.replace("^.", "ρ.");
+        final String base;
+        if (transformed.startsWith("QQ.")) {
+            base = transformed.replace("QQ", "Φ.org.eolang");
+        } else if (transformed.startsWith("Q.")) {
+            base = transformed.replace("Q.", "Φ.");
+        } else {
+            base = transformed;
+        }
+        final String result;
+        if (base.startsWith("ρ.") || base.startsWith("Φ.")) {
+            result = base;
+        } else {
+            result = String.format("ξ.ρ.%s", base);
+        }
+        return result;
+    }
+
     /**
      * Trim margin from text block.
      *
diff --git a/eo-parser/src/main/resources/org/eolang/parser/parse/auto-phi-formation-restruct.xsl b/eo-parser/src/main/resources/org/eolang/parser/parse/auto-phi-formation-restruct.xsl
index 82d13169d74..59ae84e57fb 100644
--- a/eo-parser/src/main/resources/org/eolang/parser/parse/auto-phi-formation-restruct.xsl
+++ b/eo-parser/src/main/resources/org/eolang/parser/parse/auto-phi-formation-restruct.xsl
@@ -63,5 +63,5 @@
     </xsl:copy>
   </xsl:template>
   <!-- Remove redundant ξ.X for void attributes, located inside the auto-phi formation -->
-  <xsl:template match="o[starts-with(@base,'ξ.') and ancestor::o[contains(@name,'ap🌵')][descendant::o[@base='∅' and @name=substring-after(current()/@base,'ξ.')]]]"/>
+  <xsl:template match="o[starts-with(@base,'ξ.') and not(@pos) and ancestor::o[contains(@name,'ap🌵')][descendant::o[@base='∅' and @name=substring-after(current()/@base,'ξ.')]]]"/>
 </xsl:stylesheet>
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-application-with-hyphens.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-application-with-hyphens.yaml
new file mode 100644
index 00000000000..9732d0129ca
--- /dev/null
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-application-with-hyphens.yaml
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+sheets: []
+asserts:
+  - /object[not(errors)]
+  - //o[not(@base) and @name='ap🌵34' and o[@name='φ' and @base='.as-j']/o[@base='.as-i']/o[@base='Φ.org.eolang.text']/o[@base='ξ.ρ.args']]
+  - //o[@base='.as-i' and not(@name)]/o[2][@base='Φ.org.eolang.as-bar.b']
+input: |
+  [args] > foo
+    bar > i
+      ((text args).as-i as-bar.b).as-j >> [x]
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-application-with-rho.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-application-with-rho.yaml
new file mode 100644
index 00000000000..71a5542995f
--- /dev/null
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-application-with-rho.yaml
@@ -0,0 +1,12 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+sheets: []
+asserts:
+  - /object[not(errors)]
+  - //o[not(@base) and @name='ap🌵34' and o[@name='φ' and @base='ρ.x.ρ.y.ρ.z']]
+input: |
+  [args] > main
+    a > x1
+      ^.x.^.y.^.z >> [y]
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-fqn-application.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-fqn-application.yaml
new file mode 100644
index 00000000000..7000754b4dd
--- /dev/null
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-fqn-application.yaml
@@ -0,0 +1,12 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+sheets: []
+asserts:
+  - /object[not(errors)]
+  - //o[not(@base) and @name='ap🌵34' and o[2][@name='x' and @base='∅' and not(@as)] and o[3][@name='φ' and @base='Φ.a.bca.eaa.boom']/o[1][@base='Φ.org.eolang.number']]
+input: |
+  [] > foo
+    start > @
+      Q.a.bca.eaa.boom 42 >> [x]
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-fqn-precedence-application.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-fqn-precedence-application.yaml
new file mode 100644
index 00000000000..790f553c039
--- /dev/null
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-fqn-precedence-application.yaml
@@ -0,0 +1,13 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+sheets: []
+asserts:
+  - /object[not(errors)]
+  - //o[not(@base) and @name='ap🌵34' and o[@name='φ' and @base='.j']/o[@base='.i']/o[@base='Φ.org.eolang.txt.text']/o[@base='ξ.ρ.args']]
+  - //o[@base='.i' and not(@name)]/o[2][@base='Φ.org.foo.b']
+input: |
+  [args] > main
+    foo > app
+      ((Q.org.eolang.txt.text args).i Q.org.foo.b).j >> [y]
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-nested-application.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-nested-application.yaml
new file mode 100644
index 00000000000..1a96b5df2b2
--- /dev/null
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-nested-application.yaml
@@ -0,0 +1,21 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+# @todo #4559:60min Enable the test after auto-phi formations under nested abstracts will be parsed
+#  correctly. For now, we just appending `ξ.ρ` to the application `@base`. We should not do this,
+#  instead, we keep it as `@base`, allowing XSL transformations resolve the scope correctly. This
+#  puzzle depends on this issue: https://github.com/objectionary/eo/issues/4557
+skip: true
+sheets: []
+asserts:
+  - /object[not(errors)]
+  - //o[not(@base) and @name='ap🌵68' and o[@name='φ' and @base='ξ.ρ.ρ.ρ.ρ.x.some']]
+input: |
+  [] > foo
+    5 > x
+    [] > bar
+      [] > baz
+        [] > bus
+          start > nested
+            x.some >> []
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-qq-application.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-qq-application.yaml
new file mode 100644
index 00000000000..f4997fef20d
--- /dev/null
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-from-qq-application.yaml
@@ -0,0 +1,12 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+sheets: []
+asserts:
+  - /object[not(errors)]
+  - //o[not(@base) and @name='ap🌵34' and o[2][@name='x' and @base='∅' and not(@as)] and o[3][@name='φ' and @base='Φ.org.eolang.foo.bar']/o[1][@base='Φ.org.eolang.number']]
+input: |
+  [] > main
+    start > @
+      QQ.foo.bar 42 >> [x]
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-with-application-precedence.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-with-application-precedence.yaml
new file mode 100644
index 00000000000..c77fbfaf78a
--- /dev/null
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-with-application-precedence.yaml
@@ -0,0 +1,21 @@
+# SPDX-FileCopyrightText: Copyright (c) 2016-2025 Objectionary.com
+# SPDX-License-Identifier: MIT
+---
+# yamllint disable rule:line-length
+sheets: []
+asserts:
+  - /object[not(errors)]
+  - //o[not(@base) and @name='ap🌵34' and o[@name='φ' and @base='.ttt']/o[@base='.what']/o[@base='Φ.org.eolang.text']/o[@base='ξ.ρ.orgn']]
+  - //o[not(@base) and @name='ap🌵54' and o[@name='φ' and @base='.g']/o[@base='.e']/o[@base='.c']]
+  - //o[not(@base) and @name='ap🌵86' and o[@name='φ' and @base='.contains']/o[@base='Φ.org.eolang.text']/o[@base='ξ.ρ.orgn']]
+  - //o[not(@base) and @name='ap🌵86' and o[@name='φ' and @base='.contains']/o[@base='ξ.x']]
+input: |
+  [cont-list] > custom-map
+    foo > boom
+      ((text orgn).what b).ttt >> [y]
+    bar > dummy
+      (((a b).c d).e f).g >> [v]
+    mapped. > @
+      cont-list
+        (text orgn).contains x >> [x]
+    origin > orgn!
diff --git a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-with-nested-vapplication.yaml b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-with-nested-vapplication.yaml
index 0d12aeaa677..793f4ac3b23 100644
--- a/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-with-nested-vapplication.yaml
+++ b/eo-parser/src/test/resources/org/eolang/parser/eo-syntax/auto-phi-formation-with-nested-vapplication.yaml
@@ -5,8 +5,8 @@
 sheets: []
 asserts:
   - /object[not(errors)]
-  - //o[not(@base) and @name='a🌵34' and o[2][@name='i' and @base='∅'] and o[3][@name='φ']]
-  - //o[@base='Φ.org.eolang.foo' and o[@base='ξ.a🌵34']]
+  - //o[not(@base) and @name='ap🌵34' and o[2][@name='i' and @base='∅'] and o[3][@name='φ']]
+  - //o[@base='Φ.org.eolang.foo' and o[@base='ξ.ap🌵34']]
 input: |
   [] > main
     foo > @