Old San Juan’s Secrets: A Journey Through Crypts, Cathedrals, and Hidden Architecture

Old San Juan is often known for its iconic blue cobblestones, colorful buildings, and imposing fortresses, but a city with more than 500 years of legacy holds far more than what first meets the eye. Beneath the postcard views lie deeper stories: stone-carved staircases tucked inside ancient walls, the careful details of the oldest stained-glass window in Puerto Rico, and crypts that rest quietly beneath centuries-old churches. These aren’t just relics—they’re Old San Juan’s secrets woven into the city’s very foundation, waiting to be admired. For those willing to wander off the beaten path in Old San Juan, the rewards are rich in history and wonder. Caring for these treasures isn’t just about honoring history—it’s also a sustainable act. Preserving instead of rebuilding helps reduce environmental impact, prevent waste, and minimize the need for resource-intensive materials. In many ways, protecting the past is one of the most forward-thinking things we can do.

Unlocking Old San Juan’s Secrets with a Local Historian

That’s why exploring beyond the well-trodden paths takes on new meaning—it’s not just about seeing more, but about understanding why these spaces matter. And that curiosity to go beyond the most visited spots in Old San Juan is exactly what brought us here.

Our journey begins with Andy Rivera, an architect and historian whose deep knowledge and passion for architectural heritage opened doors (and staircases) we might have otherwise walked right past, missing the Old San Juan’s secrets and treasures found inside. What began as a simple Facebook page, where he shared detailed insights about historic buildings in Old San Juan and beyond, quickly grew into something much larger. His dedication eventually led him to create the Puerto Rico Historic Building Drawings Society, a group committed to offering educational tours that weave together architectural detail and historical storytelling, bringing the Island’s history to life.

Thanks to Andy, our group wasn’t just sightseeing. We were time-traveling through Old San Juan.

Hidden Rooms Behind the Cathedral Walls

We meet up with him early in the morning in front of the steps of the Catedral de San Juan Bautista. Tucked into the heart of Calle del Cristo, perfectly aligned with the ancient Puerta de San Juan, the cathedral stands elegant and eternal. Its cream-colored façade, arched doorways, and bell tower crowned with a cross give it a restrained beauty. It’s the largest Christian church in Puerto Rico, and the second oldest on the Island. More than five centuries of prayers, footsteps, and sacred silence live within its walls—one of many old San Juan secrets hidden in plain sight.

Inside, the mood shifts. Light filters through vibrant stained-glass, spilling color onto vaulted Gothic ceilings, arched arcades, and chapels adorned with golden frescoes. Andy walks us along the right side of the nave, leading us past the Capilla de San Pío I, to a pair of large wooden doors that are cordoned off to prevent access. But he removes the barrier with ease, and because we’re touring with him, we get special access and step inside. The room holds sacred relics of Saint Pius, the ninth pope of the Catholic Church, along with ornaments and vestments worn by Pope John Paul II during his visit to Puerto Rico in 1984.

Over the years, the space has become a place for preserving and showcasing sacred items—from priestly vestments and processional crosses to gold candlesticks and even ornately decorated mitres, the traditional ceremonial headdress worn by bishops.

“But this isn’t what we came to see,” he gestures toward a door I hadn’t noticed, nearly hidden in the back wall. It looks like any other. Until he opens it.

“Follow me!”

We follow him into a stone chamber unlike any I’ve ever seen.

The room is solemn, silent. Rows of urns rest behind glass, some crafted from stainless steel, others in shimmering crystal, vibrant pinks and intricate designs marking the lives once lived. It’s part crypt, part mausoleum—a place of memory, chosen by families who wanted their loved ones to rest beneath the church’s protection.

Above us, the architecture screams of the past. The ceiling rises in classic Gothic ribbed vaults, where pointed arches and decorative keystones create a pattern of stone lace. Tall, narrow windows filter sunlight in soft beams, casting a warm, golden hue across the walls. As our guide recounts, the first structure of the cathedral was built in wood in 1526, but part of it was destroyed after a storm passed through town. It wasn’t until 1540 that the church began to take the form it has today, with a solid stone foundation. I stand still, realizing we’re surrounded by ashes, and the room goes quiet in respect.

“We’re almost there,” Andy's voice breaks the quiet, opening yet another door. We step into a dimly lit storage room, cluttered with decades of forgotten things—old holiday decorations, dusty tables, mismatched chairs. The kind of place most people pass by without a second glance—a humbling reminder of the real treasures of Old San Juan that often lie far off the beaten path. But Andy walks with purpose, navigating the chaos like a man following a map only he can see. At the far end of the room, he stops.

“This,” he says, “is what we came to see.”

He pulls aside a curtain of shadow to reveal a narrow stone entrance—and just beyond it, carved into the bones of the building, one of the most fascinating Old San Juan secrets: a spiral staircase chiseled by hand more than a century ago.

A Twist of Stone and Time

The staircase isn’t what I expected. It isn’t grand or gilded—no ornate railings or polished marble steps. No, this was something much more powerful: a spiral of solid stone made by the hands of Old San Juan’s past residents, worn smooth by centuries of footsteps. 

The staircase coils upward like a seashell, hidden within the very bones of the cathedral. The stone is soft in color—earthy, worn, almost golden in patches where sunlight touches it. In some places, the edges have softened from wear, and a fine patina of age darkens the inner curve, where hands must have brushed for balance over the years. One particularly beautiful detail is the twist of the central column.

Climbing it feels intimate. You have to lean in and hold on to the railing. “Notice how the railing isn’t added on,” Andy points out. “It’s carved directly from the stone. Part of it.” I reach out to touch it, it’s cold and smooth to the touch—clearly part of the stone itself.

About halfway up, I pause to look out at the city through a narrow window, where light pours in gently, brushing against the curve of the central column. The chisel marks of long-gone hands are still visible if you look closely, etched into the stone like quiet signatures. “The windows are narrow on the outside and wider on the inside—like a funnel—to let air flow better into the building,” Andy explains.

At the top, the staircase opens into daylight. The rooftop of the cathedral stretches out beneath the blue Caribbean sky. The bells loom above, still and massive, and around them, Old San Juan spills out in every direction—terracotta roofs and painted balconies. And yet, after soaking it in, I find myself drawn back to the staircase.

Because it’s in places like this—those off the beaten path Old San Juan gems—where conservation becomes not just important, but essential. These aren’t just stairs. They’re memories, carved in stone. They’re passages through memory, carved by ancestors—and now, I get to walk among them. Preserving them means preserving our ability to walk with the past.

The Oldest Stained-Glass Window in Puerto Rico

As we start to head out of the cathedral, Andy suddenly pauses. “Before we go,” he says, “there’s something important you should see.” Intrigued, we follow him down the right side of the nave, where the light grows softer and the space takes on a quieter, more intimate feel. He stops before a vibrant stained-glass window.

“The Catedral de San Juan Bautista holds many treasures, like the remains of the explorer and first governor of Puerto Rico, Juan Ponce de León. But one of the most captivating is this,” he says, pointing to a stained-glass window tucked inside one of the quiet chapels. “This,” he says, “is ‘Las Ánimas en el Purgatorio’—the oldest stained glass window in Puerto Rico. It was brought from Spain in 1850.”

I step in front of it, letting the colored light wash over me—just as it has for nearly two centuries. The window is a vivid composition of light and emotion. At its center, a radiant Virgin Mary, robed in blue and surrounded by golden light, is lifted heavenward by a host of angels. Below her, the souls in purgatory reach upward with pleading eyes, wrapped in swirls of flame and shadow. The color palette is striking: rich reds, deep blues, and luminous golds that seem to catch fire when sunlight pours through. The scene is vivid. Alive. And yet silent in the way only sacred things can be.

In Catholic tradition, the ánimas refer to the souls in purgatory—those of the deceased who are saved but still need to be purified of minor sins before entering heaven. It is believed that the living can help them through prayers and the celebration of Masses. Standing there, washed in colored light, I wonder how many prayers have been whispered in front of this very window.

After leaving the cathedral, we trek along the blue cobblestone streets to the highest point of Old San Juan, where Iglesia San José is perched like a quiet guardian watching over the city’s evolution. Founded in 1532, it holds the title of Puerto Rico’s oldest church and the second oldest in the Americas—another one of Old San Juan's off-the-beaten-path treasures.

After nearly two decades of meticulous restoration using techniques and materials faithful to the 16th century, the church has regained much of its original grandeur and is now finally open to the public. Inside, the cool air carries the scent of limestone and history. Gothic arches stretch overhead, flanked by double vaults, stained glass windows, and walls adorned with religious paintings, carved saints, and stone sculptures. 

It’s truly breathtaking.

The Hidden Crypt of Iglesia San José

We walk into a chapel located on the right side of the nave. Wooden pews are arranged in neat rows. The altar is simple, adorned with intricate carvings, and a serene statue of the Virgin and Child, nestled in a soft alcove, overlooks the space. It feels peaceful.

Until Andy gestures to where I’m standing. “Mind stepping aside?” he asks gently. I move—then realize I had been standing on top of a square panel set into the floor. Andy finds the latch, lifts the wooden hatch, and reveals a narrow staircase descending into darkness: the crypt entrance.

“This,” he says, “is the crypt.”

I freeze. I wouldn’t have stood there if I’d known!

“Who wants to go in first?” he jokes.

Tales of the Hidden Crypt

The contrast between the peaceful, sacred space above and the mystery below is almost cinematic. Andy tells us this was once the resting place of Puerto Rico’s first governors—though their remains were later moved. Still, the crypt remains. 

As I descend slowly the stone steps into the crypt—narrow and worn—I feel a subtle shift in the air: hotter, humid, and a little harder to breathe. With every step, the light from the chapel above fades, replaced by the dim glow of our cellphone flashlights. As I move the light around, I get a better look—the crypt is a quiet, earth-toned chamber carved into the stone beneath the church. I wonder if we were disturbing any ghosts of the governor's past.

Along the walls are arched niches, stacked in rows, built of brick and lined with worn white plaster. Each one once held human remains. Some are sealed, others left open, revealing the raw texture of the bricks within.

We climb back up the narrow steps, leaving the crypt behind and emerging once more into the soft light of the chapel. We move past flickering candles and shadowed arches, the silence hanging just a little heavier now. Outside, the sunlight feels almost too bright. We thank Andy quietly, and just like that, the doors close behind us—sealing the secrets back inside. Each of us walks away carrying a little more history—and a trace of something we can’t quite name.

Thanks to Andy, we didn’t just learn about the city’s history—we walked through it, touched it, and descended into it. And in doing so, we discovered that this city isn’t just preserved.

It’s alive.