diff --git a/lld/ELF/LinkerScript.cpp b/lld/ELF/LinkerScript.cpp
--- a/lld/ELF/LinkerScript.cpp
+++ b/lld/ELF/LinkerScript.cpp
@@ -1179,7 +1179,11 @@
 
   Out::elfHeader->ptLoad = nullptr;
   Out::programHeaders->ptLoad = nullptr;
-  firstPTLoad->firstSec = findFirstSection(firstPTLoad);
+  llvm::erase_if(firstPTLoad->sections, [](const OutputSection *s) {
+    return s == Out::elfHeader || s == Out::programHeaders;
+  });
+  firstPTLoad->firstSec =
+      firstPTLoad->sections.empty() ? nullptr : firstPTLoad->sections.front();
 
   llvm::erase_if(phdrs,
                  [](const PhdrEntry *e) { return e->p_type == PT_PHDR; });
diff --git a/lld/ELF/Writer.h b/lld/ELF/Writer.h
--- a/lld/ELF/Writer.h
+++ b/lld/ELF/Writer.h
@@ -33,6 +33,7 @@
       : p_align(type == llvm::ELF::PT_LOAD ? config->maxPageSize : 0),
         p_type(type), p_flags(flags) {}
   void add(OutputSection *sec);
+  void finalize();
 
   uint64_t p_paddr = 0;
   uint64_t p_vaddr = 0;
@@ -43,6 +44,7 @@
   uint32_t p_type = 0;
   uint32_t p_flags = 0;
 
+  std::vector<OutputSection *> sections;
   OutputSection *firstSec = nullptr;
   OutputSection *lastSec = nullptr;
   bool hasLMA = false;
diff --git a/lld/ELF/Writer.cpp b/lld/ELF/Writer.cpp
--- a/lld/ELF/Writer.cpp
+++ b/lld/ELF/Writer.cpp
@@ -1078,6 +1078,17 @@
   p_align = std::max(p_align, sec->alignment);
   if (p_type == PT_LOAD)
     sec->ptLoad = this;
+  sections.push_back(sec);
+}
+
+void PhdrEntry::finalize() {
+  if (sections.empty())
+    return;
+  llvm::stable_sort(sections, [](OutputSection *l, OutputSection *r) {
+    return l->addr < r->addr;
+  });
+  firstSec = sections.front();
+  lastSec = sections.back();
 }
 
 // The beginning and the ending of .rel[a].plt section are marked
@@ -2211,6 +2222,12 @@
   // of finalizing other sections.
   for (OutputSection *sec : outputSections)
     sec->finalize();
+
+  // Sort segment sections by address. For one segment, we layout sections in
+  // the order of addresses.
+  for (Partition &part : partitions)
+    for (PhdrEntry *p : part.phdrs)
+      p->finalize();
 }
 
 // Ensure data sections are not mixed with executable sections when
@@ -2631,11 +2648,7 @@
       if (p->p_type == PT_LOAD && (p->p_flags & PF_X))
         lastRX = p;
 
-  // Layout SHF_ALLOC sections before non-SHF_ALLOC sections. A non-SHF_ALLOC
-  // will not occupy file offsets contained by a PT_LOAD.
-  for (OutputSection *sec : outputSections) {
-    if (!(sec->flags & SHF_ALLOC))
-      continue;
+  auto placeSection = [&](OutputSection *sec) {
     off = setFileOffset(sec, off);
 
     // If this is a last section of the last executable segment and that
@@ -2644,9 +2657,27 @@
     if (config->zSeparate != SeparateSegmentKind::None && lastRX &&
         lastRX->lastSec == sec)
       off = alignTo(off, config->commonPageSize);
-  }
+  };
+
+  // If a linker script is in use sections can be at arbitrary addresses and
+  // can be interleaved across segments. We handle this by placing output
+  // sections in load segment order. The sections in the segment are already
+  // sorted by address.
+  if (script->hasPhdrsCommands())
+    for (Partition &part : partitions)
+      for (PhdrEntry *p : part.phdrs)
+        for (OutputSection *sec : p->sections)
+          if (sec != Out::elfHeader && !sec->offset)
+            placeSection(sec);
+
+  // Layout SHF_ALLOC sections before non-SHF_ALLOC sections. A non-SHF_ALLOC
+  // will not occupy file offsets contained by a PT_LOAD.
+  // Skip sections which are already assigned an offsets.
+  for (OutputSection *sec : outputSections)
+    if ((sec->flags & SHF_ALLOC) && !sec->offset)
+      placeSection(sec);
   for (OutputSection *sec : outputSections)
-    if (!(sec->flags & SHF_ALLOC))
+    if (!sec->offset)
       off = setFileOffset(sec, off);
 
   sectionHeaderOff = alignTo(off, config->wordsize);
diff --git a/lld/test/ELF/linkerscript/implicit-program-header.test b/lld/test/ELF/linkerscript/implicit-program-header.test
--- a/lld/test/ELF/linkerscript/implicit-program-header.test
+++ b/lld/test/ELF/linkerscript/implicit-program-header.test
@@ -7,7 +7,7 @@
 # RUN: llvm-readelf -l %t1 | FileCheck %s
 
 # CHECK:      Segment Sections...
-# CHECK-NEXT:   00     .dynsym .hash .dynstr .foo .text .dynamic
+# CHECK-NEXT:   00     .dynsym .hash .dynstr .text .dynamic
 # CHECK-NEXT:   01     .foo
 # CHECK-NEXT:   02     .foo
 
diff --git a/lld/test/ELF/linkerscript/out-of-order-sections.s b/lld/test/ELF/linkerscript/out-of-order-sections.s
new file mode 100644
--- /dev/null
+++ b/lld/test/ELF/linkerscript/out-of-order-sections.s
@@ -0,0 +1,31 @@
+# REQUIRES: x86
+# RUN: split-file %s %t
+# RUN: llvm-mc -filetype=obj -triple=x86_64-unknown-linux %t/test.s -o %t.o
+# RUN: ld.lld -o %t1 --script %t/test.lds %t.o
+# RUN: llvm-readelf -l %t1 | FileCheck %s
+
+# CHECK:      Type Offset   VirtAddr           PhysAddr           FileSiz  MemSiz   Flg Align
+# CHECK-NEXT: LOAD 0x001000 0x0000000000001000 0x0000000000001000 0x001001 0x001001 R E 0x1000
+# CHECK-NEXT: LOAD 0x003000 0x0000000000000000 0x0000000000000000 0x000001 0x000001 R   0x1000
+
+#--- test.s
+.global _start
+_start:
+ nop
+
+.section .foo, "a"
+ .byte 0
+
+.section .bar, "a"
+ .byte 0
+
+#--- test.lds
+PHDRS {
+	ph1 PT_LOAD;
+	ph2 PT_LOAD;
+}
+SECTIONS {
+	.text 0x2000 : {*(.text*)} :ph1
+	.foo 0 : {*(.foo*)} :ph2
+	.bar 0x1000 : {*(.bar*)} :ph1
+}
diff --git a/lld/test/ELF/linkerscript/sections-va-overflow.test b/lld/test/ELF/linkerscript/sections-va-overflow.test
--- a/lld/test/ELF/linkerscript/sections-va-overflow.test
+++ b/lld/test/ELF/linkerscript/sections-va-overflow.test
@@ -18,5 +18,5 @@
 ## with VA 0xffffffff20000000. That might be technically correct, but most probably
 ## is a result of a broken script file and causes file offset calculation overflow.
 ## It seems we do not have to support it, so we don't and we report an error in this case.
-# ERR: error: unable to place section .text at file offset [0xFFFFFFFF20000000, 0xFFFFFFFF20000000]; check your linker script for overflows
+# ERR: error: output file too large: 18446744069951455872 bytes
 # ERR-NOT: unable to place section .bss