The conservatory divides its interior into five distinct worlds. The Bromeliad House features a wrought iron display tree, designed by Randy Benson and crafted by local ironworkers, from which dozens of Tillandsia species hang like aerial sculptures. The Fern House contains not only ferns but also a collection of carnivorous plants, Venus fly traps, sundews, and pitcher plants arranged in bog gardens that replicate the acidic wetlands these predators call home. The Seasonal House reinvents itself six times a year, cycling through poinsettias, azaleas, hydrangeas, fuchsias, and other flowers matched to the calendar. The Palm House shelters a Windmill Palm donated from the Hiram Chittenden Locks around 1953 and a Sago Palm that was roughly 80 years old as of 2009. And the Cacti and Succulent House holds a Jade Tree grown from a cutting taken in 1916, making it one of the oldest living residents of the building.

The conservatory holds a quiet distinction: it is a registered United States Fish and Wildlife Service repository for confiscated plants. When federal agents intercept illegally transported orchids, cycads, or other protected species at ports and borders, the specimens can end up here. The orchid collection itself dates to 1921, when Mrs. Anna H. Clise donated the founding specimens. It has grown to include representatives of the largest orchid genera, Bulbophyllum, Epidendrum, and Dendrobium, alongside popular cultivated varieties like Cattleya and Phalaenopsis. Transporting endangered orchids across international lines violates the Convention on International Trade in Endangered Species, and over the years, many confiscated specimens have found a second life behind these glass walls. The conservatory quietly serves as both a botanical garden and a kind of witness protection program for plants.

In 2005, 2008, and again in 2014, the conservatory became the center of citywide fascination when its corpse flower bloomed. The corpse flower, Amorphophallus titanum, is one of the largest flowering plants on earth and one of the rarest to see in bloom, typically flowering only two to three times within its 40-year lifespan. The conservatory's specimen, nicknamed Waldo, drew enormous crowds. Before its 2008 bloom, Waldo measured 47 and a half inches tall, 30 inches wide, and 52 and a half inches long. The 2014 flowering prompted Seattle Mayor Ed Murray to officially proclaim "Corpse Flower Week." The bloom lasts only a day or two, and the plant's signature smell, the stench of rotting flesh designed to attract pollinating beetles and flies, made each event as viscerally memorable as it was botanically significant. More than 150,000 people visit the conservatory in a typical year, but during corpse flower events, the lines stretched down the park paths.

By 1978, the conservatory was falling apart. Its glass panes and wood-and-iron framework had deteriorated to the point that the building had to close during high winds. Seattle citizens campaigned to save the structure, and the Friends of the Conservatory formed as a nonprofit in 1980. Working with Seattle Parks and Recreation, the group funded an architectural restoration between 1980 and 1985 that preserved the original Victorian character while making the building structurally sound. In 2004, when the city proposed a mandatory five-dollar admission fee, the Friends organized a community drive that defeated the measure. The conservatory remains free to enter. The original beveled glass lunette window above the main entry, the only surviving wood-and-glass element from 1912 after two major renovations, was restored in 2000. In 1981, artist Richard Spaulding added a hand-blown stained glass canopy called "Homage in Green" to the vestibule, blending contemporary craft with the building's Victorian bones. Over 100 volunteers contribute more than 2,500 hours of service annually, keeping this glass cathedral of plants alive.