diff --git a/lld/ELF/Writer.cpp b/lld/ELF/Writer.cpp
--- a/lld/ELF/Writer.cpp
+++ b/lld/ELF/Writer.cpp
@@ -2624,22 +2624,47 @@
       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;
-    off = setFileOffset(sec, off);
+  // Place output sections which are part of load segments first, but include
+  // empty sections in address order. This means that section order does not
+  // need to match segment order (which can happen when using a link script)
+  // while avoiding confusing discontinuities in file offsets.
+  for (Partition &part : partitions) {
+    for (PhdrEntry *p : part.phdrs) {
+      if (p->p_type != PT_LOAD)
+        continue;
 
-    // If this is a last section of the last executable segment and that
-    // segment is the last loadable segment, align the offset of the
-    // following section to avoid loading non-segments parts of the file.
-    if (config->zSeparate != SeparateSegmentKind::None && lastRX &&
-        lastRX->lastSec == sec)
-      off = alignTo(off, config->commonPageSize);
+      // Write out sections which have no file data to maintain section order
+      // as much as possible. Do this until we encounter a section with a
+      // different load segment to the one we're currently writing.
+      bool write_empty = true;
+      for (OutputSection *sec : outputSections) {
+        if (sec->offset)
+          continue;
+        if (sec->ptLoad && sec->ptLoad != p) {
+          write_empty = false;
+          continue;
+        }
+        if (write_empty && (sec->type == SHT_NOBITS || !sec->size)) {
+          off = setFileOffset(sec, off);
+          continue;
+        }
+        if (sec->ptLoad != p)
+          continue;
+        off = setFileOffset(sec, off);
+
+        // If this is a last section of the last executable segment and that
+        // segment is the last loadable segment, align the offset of the
+        // following section to avoid loading non-segments parts of the file.
+        if (config->zSeparate != SeparateSegmentKind::None && lastRX &&
+            lastRX->lastSec == sec)
+          off = alignTo(off, config->commonPageSize);
+      }
+    }
   }
+
+  // Then place remaining sections
   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 +1,49 @@
+# REQUIRES: x86
+# RUN: llvm-mc -filetype=obj -triple=x86_64-unknown-linux %s -o %t
+# RUN: echo "PHDRS { \
+# RUN:           ph1 PT_LOAD; \
+# RUN:           ph2 PT_LOAD; } \
+# RUN:       SECTIONS { \
+# RUN:           .text 0 : {*(.text*)} :ph1 \
+# RUN:           .foo 0x4000 : {*(.foo*)} :ph2 \
+# RUN:           .bar 0x1000 : {*(.bar*)} :ph1 }" > %t.script
+# RUN: ld.lld -o %t1 --script %t.script %t
+# RUN: llvm-readobj -l %t1 | FileCheck %s
+
+# CHECK:     ProgramHeaders [
+# CHECK-NEXT:  ProgramHeader {
+# CHECK-NEXT:    Type: PT_LOAD (0x1)
+# CHECK-NEXT:    Offset: 0x1000
+# CHECK-NEXT:    VirtualAddress: 0x0
+# CHECK-NEXT:    PhysicalAddress: 0x0
+# CHECK-NEXT:    FileSize: 4097
+# CHECK-NEXT:    MemSize: 4097
+# CHECK-NEXT:    Flags [ (0x5)
+# CHECK-NEXT:      PF_R (0x4)
+# CHECK-NEXT:      PF_X (0x1)
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Alignment: 4096
+# CHECK-NEXT:  }
+# CHECK-NEXT:  ProgramHeader {
+# CHECK-NEXT:    Type: PT_LOAD (0x1)
+# CHECK-NEXT:    Offset: 0x3000
+# CHECK-NEXT:    VirtualAddress: 0x4000
+# CHECK-NEXT:    PhysicalAddress: 0x4000
+# CHECK-NEXT:    FileSize: 1
+# CHECK-NEXT:    MemSize: 1
+# CHECK-NEXT:    Flags [ (0x4)
+# CHECK-NEXT:      PF_R (0x4)
+# CHECK-NEXT:    ]
+# CHECK-NEXT:    Alignment: 4096
+# CHECK-NEXT:  }
+# CHECK-NEXT: ]
+
+.global _start
+_start:
+ nop
+
+.section .foo, "a"
+ .byte 0
+
+.section .bar, "a"
+ .byte 0
diff --git a/lld/test/ELF/partition-notes.s b/lld/test/ELF/partition-notes.s
--- a/lld/test/ELF/partition-notes.s
+++ b/lld/test/ELF/partition-notes.s
@@ -37,7 +37,7 @@
 // CHECK-NEXT:       Owner: GNU
 // CHECK-NEXT:       Data size:
 // CHECK-NEXT:       Type: NT_GNU_BUILD_ID (unique build ID bitstring)
-// CHECK-NEXT:       Build ID: 08b93eab87177a2356d1b0d1148339463f98dac2
+// CHECK-NEXT:       Build ID: 90633653e589c06ee0c7e99559054d460cfc4294
 // CHECK-NEXT:     }
 // CHECK-NEXT:   }
 // CHECK-NEXT: ]
diff --git a/lld/test/ELF/partition-synthetic-sections.s b/lld/test/ELF/partition-synthetic-sections.s
--- a/lld/test/ELF/partition-synthetic-sections.s
+++ b/lld/test/ELF/partition-synthetic-sections.s
@@ -190,9 +190,9 @@
 // FILL-NEXT: *
 // FILL-NEXT: 002000
 
-// FILL: 004010 cccc cccc cccc cccc cccc cccc cccc cccc
+// FILL: 005010 cccc cccc cccc cccc cccc cccc cccc cccc
 // FILL-NEXT: *
-// FILL-NEXT: 005000
+// FILL-NEXT: 006000
 
 .section .llvm_sympart,"",@llvm_sympart
 .asciz "part1"