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Quarto vs R Markdown in 2026: Which Should You Use?

· 5 min read · Updated March 13, 2026 · intermediate
r quarto rmarkdown reproducible-research reporting

R Markdown has been the backbone of reproducible research in R for over a decade. Quarto, released in 2022, is now positioned as its official successor. If you are still using R Markdown, or if you are starting fresh, understanding the differences matters for your workflow.

This guide compares Quarto and R Markdown as they stand in 2026, with practical guidance on which to choose.

The Short Answer

Use Quarto for new projects. It is actively developed, supports more languages and output formats, and has a cleaner architecture. R Markdown is not going away—millions of documents exist and will continue to work—but new features come to Quarto first.

That said, R Markdown still makes sense in specific situations. Let us dig into the details.

What Quarto Changes

Unified Configuration

The most immediate difference is how you configure documents. In R Markdown, you often needed a separate setup chunk to set chunk options:

```{r setup, include=FALSE}
 knitr::opts_chunk$set(echo = TRUE, fig.width = 8)
```

In Quarto, everything goes in the YAML header:

---
title: "My Document"
format:
  html:
    echo: true
    fig-width: 8
---

This seems like a small change, but it makes documents cleaner and keeps configuration in one place. You also get editor support—IDE autocompletion for YAML options that does not exist in R Markdown.

More Output Formats

Quarto ships with more built-in output formats out of the box:

  • HTML, PDF, Word (same as R Markdown)
  • Revealjs presentations — native, no separate package needed
  • Jupyter notebooks — Quarto renders .ipynb files directly
  • Websites and blogs — built-in project types
  • Books — full documentation site generation

For R Markdown, many of these required additional packages (bookdown, blogdown, revealjs). Quarto bakes them in.

Multi-Language Support

R Markdown is R-centric. Quarto started with R but added native support for Python, Julia, and Observable JavaScript:

---
title: "Analysis"
format: html
---

This same document can run R code, Python code, and JavaScript—each in its own engine—without wrapper packages. If your team uses multiple languages, Quarto eliminates the need for separate workflows.

Better Cross-References

Quarto handles figure, table, and equation cross-references more consistently:

See @fig-density for the distribution.

```{r}
#| label: fig-density
#| fig-cap: "Density Plot"
plot(density(x))
```

The #| syntax (inspired by Jupyter) replaces R Markdown’s chunk options with a cleaner format that works across languages.

Where R Markdown Still Wins

Package Dependencies

R Markdown lives in the rmarkdown package, which has been stable for years. Quarto is a separate installation—a standalone CLI tool that runs independently of R. Some environments (like certain RStudio Server configurations) make installing Quarto tricky.

If you are in a restricted environment where you cannot install external tools, R Markdown remains the practical choice.

Legacy Documents

If you have an existing R Markdown project with dozens or hundreds of documents, migrating to Quarto is not trivial. The syntax differences are not huge, but cumulative migration takes time.

For maintainers of large R Markdown codebases, the question is whether the benefits justify the migration cost. In 2026, many teams are making that transition, but it is not instantaneous.

Specific Package Features

Some R Markdown extensions do not yet have Quarto equivalents. The rgl package for 3D graphics renders more reliably in R Markdown. Certain Shiny-specific features work better in R Markdown documents.

Check your specific dependencies before switching.

Feature Comparison

FeatureR MarkdownQuarto
Active developmentMaintenance modeActive
Output formatsRequires packagesBuilt-in
Multi-languageR onlyR, Python, Julia, JS
Configuration locationYAML + setup chunksYAML only
Cross-referencesVia bookdownNative
Website generationVia blogdownBuilt-in
Jupyter supportNoYes
VS Code supportLimitedFull

When to Use Each

Choose Quarto When:

  1. Starting a new project — Any new reproducible document or website should use Quarto.
  2. Building websites or books — The built-in project types are cleaner than blogdown/bookdown.
  3. Using multiple languages — Python and R in the same workflow is seamless.
  4. Wanting active development — New features and bug fixes go to Quarto first.
  5. Creating presentations — Revealjs is included without extra setup.

Choose R Markdown When:

  1. Maintaining existing projects — If it works, no need to migrate just for the sake of it.
  2. Restricted environments — Cannot install Quarto CLI.
  3. Using rgl or specific packages — Check compatibility first.
  4. Team resistance to change — Migration has a learning curve.

Migration Path

If you decide to migrate, the good news is that most R Markdown documents work with minimal changes:

  1. Install Quarto — Download from quarto.org
  2. Render with Quarto — quarto render document.Rmd often works directly
  3. Update chunk options — Convert {#r chunk-label, option=value} to #| label: chunk-label, option: value
  4. Move YAML options — Pull knitr::opts_chunk$set() settings into the YAML header

RStudio and Posit Connect have built-in migration guides that handle many of these automatically.

What You Should Do

  1. Use Quarto for all new work — It is the future, and the investment pays off.
  2. Migrate when convenient — Do not rush, but plan to move existing projects over time.
  3. Check package compatibility — Before migrating, verify your critical packages work with Quarto.
  4. Learn the YAML configuration — It is cleaner than setup chunks once you get used to it.
  5. Explore built-in formats — Websites, books, and presentations are easier in Quarto.

Quarto is not just R Markdown 2.0—it is a different philosophy that unifies computational documents across languages. The transition is worth it for most users in 2026.

See Also