diff --git a/CHANGELOG.md b/CHANGELOG.md
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,3 +1,21 @@
+## 0.3.12.2
+
+-   Make section numbering more consistent with pandoc
+
+    If the first heading in your document is level 2 or more, pandoc will assign
+    index `0` to the implicit sections. Pandoc-crossref, on the other hand,
+    assinged index `1` to these sections previously. This could lead to an
+    off-by-one discrepancy between section and reference indices when using
+    pandoc's `--number-sections`.
+
+    This behaviour is now aligned with pandoc, i.e. missing top-level sections
+    will get index of `0`.
+
+    The old behaviour is kept when using pandoc-crossref's `numberSections`,
+    for backwards compatibility and also because having references start with
+    `0` is rather impractical to begin with.
+
+
 ## 0.3.12.1
 
 -   Fix docx tableEqns
diff --git a/docs/index.md b/docs/index.md
--- a/docs/index.md
+++ b/docs/index.md
@@ -255,6 +255,12 @@
 `numberSections` controls if pandoc-crossref handles numbering sections,
 while `sectionsDepth` controls what sections are numbered.
 
+Additionally, with `numberSections`, if the first heading in your document is
+level 2 or more, pandoc-crossref will assume you meant to have implicit
+headings with previous levels, and will assign those phantom implicit headings
+the index `1`. Without `numberSections`, the behaviour is consistent with
+pandoc, that is, missing headings will be assigned the index `0`.
+
 Set `sectionsDepth` to `0` to make section numbering consistent with
 `chaptersDepth`.
 
@@ -486,7 +492,9 @@
     corresponding to header numbers, e.g. `fig. 1.4.3`.
 -   `numberSections`, default `false`: if True, pandoc-crossref will
     prepend section number to section titles (as counted by
-    pandoc-crossref itself).
+    pandoc-crossref itself). This also makes pandoc-crossref assign missing
+    top-level headings the index of `1` instead of `0` to avoid ugly `sec.
+    0.0.1` references.
 -   `sectionsDepth`, default `0`:
     -   sectionsDepth \< 0 -- number all sections
     -   sectionsDepth == 0 -- be consistent with `chaptersDepths`
diff --git a/lib-internal/Text/Pandoc/CrossRef/References/Blocks.hs b/lib-internal/Text/Pandoc/CrossRef/References/Blocks.hs
--- a/lib-internal/Text/Pandoc/CrossRef/References/Blocks.hs
+++ b/lib-internal/Text/Pandoc/CrossRef/References/Blocks.hs
@@ -89,7 +89,9 @@
             inc l = let i = fst (last l) + 1 in init l <> [(i, cl i)]
             cc' | ln > n = inc $ take n cc
                 | ln == n = inc cc
-                | otherwise = cc <> take (n-ln-1) (zip [1,1..] $ repeat Nothing) <> [(1,cl 1)]
+                | otherwise = cc <> take (n-ln-1) implicitChapters <> [(1,cl 1)]
+            implicitChapters | numberSections opts = repeat (1, Nothing)
+                             | otherwise = repeat (0, Nothing)
         in cc'
       when ("sec:" `T.isPrefixOf` label') $ do
         index  <- use curChap
diff --git a/pandoc-crossref.cabal b/pandoc-crossref.cabal
--- a/pandoc-crossref.cabal
+++ b/pandoc-crossref.cabal
@@ -4,10 +4,10 @@
 --
 -- see: https://github.com/sol/hpack
 --
--- hash: 44cad1985e34691bb2ecdb6ccac537a1eb9de77329edf1dbfbdbb485ca98e803
+-- hash: 643ffe23ec490430a946bbeec84db2ff503e9b935182801185089d7fba7cdc3f
 
 name:           pandoc-crossref
-version:        0.3.12.1
+version:        0.3.12.2
 synopsis:       Pandoc filter for cross-references
 description:    pandoc-crossref is a pandoc filter for numbering figures, equations, tables and cross-references to them.
 category:       Text
@@ -110,7 +110,7 @@
   build-depends:
       base >=4.11 && <5
     , mtl >=1.1 && <2.3
-    , pandoc >=2.10 && <2.17
+    , pandoc >=2.10 && <2.18
     , pandoc-crossref-internal
     , pandoc-types >=1.21 && <1.23
     , text >=1.2.2 && <1.3
@@ -145,7 +145,7 @@
     , microlens-mtl >=0.2.0.1 && <0.3.0.0
     , microlens-th >=0.4.3.10 && <0.5.0.0
     , mtl >=1.1 && <2.3
-    , pandoc >=2.10 && <2.17
+    , pandoc >=2.10 && <2.18
     , pandoc-types >=1.21 && <1.23
     , roman-numerals ==0.5.*
     , syb >=0.4 && <0.8
@@ -167,7 +167,7 @@
     , gitrev >=1.3.1 && <1.4
     , open-browser ==0.2.*
     , optparse-applicative >=0.13 && <0.17
-    , pandoc >=2.10 && <2.17
+    , pandoc >=2.10 && <2.18
     , pandoc-crossref
     , pandoc-types >=1.21 && <1.23
     , template-haskell >=2.7.0.0 && <3.0.0.0
@@ -186,7 +186,7 @@
     , directory >=1 && <1.4
     , filepath >=1.1 && <1.5
     , hspec >=2.4.4 && <3
-    , pandoc >=2.10 && <2.17
+    , pandoc >=2.10 && <2.18
     , pandoc-crossref
     , pandoc-types >=1.21 && <1.23
     , text >=1.2.2 && <1.3
@@ -212,7 +212,7 @@
     , hspec >=2.4.4 && <3
     , microlens >=0.4.12.0 && <0.5.0.0
     , mtl >=1.1 && <2.3
-    , pandoc >=2.10 && <2.17
+    , pandoc >=2.10 && <2.18
     , pandoc-crossref
     , pandoc-crossref-internal
     , pandoc-types >=1.21 && <1.23
@@ -232,7 +232,7 @@
   build-depends:
       base >=4.11 && <5
     , criterion >=1.5.9.0 && <1.6
-    , pandoc >=2.10 && <2.17
+    , pandoc >=2.10 && <2.18
     , pandoc-crossref
     , pandoc-types >=1.21 && <1.23
     , text >=1.2.2 && <1.3