The Peter and Paul Cathedral served as the necropolis of the Romanov House, created in the image of the burial places of the Moscow Grand Princes and Tsars in the Archangel Cathedral, and the tsarinas in the Ascension Monastery of the Kremlin. The first reliably known burial dates back to May 27, 1715, when their 2-year-old daughter Natalia was buried here in the presence of Peter I and Catherine. In the northeastern part of the cathedral, graves of other children of Peter who died in infancy appeared at different times, and in 1728—his daughter Anna. At the entrance to the cathedral, on the site of the future chapel of the Great Martyr Catherine, on January 7, 1716, the body of Tsarina Marfa Matveyevna was laid to rest.

Under the still unfinished bell tower during the reign of Peter I were buried Crown Princess Charlotte Sophia Christina of Wolfenbüttel, wife of Tsarevich Alexei, the tsarevich himself who was killed, and the emperor’s sister, Maria Alexeevna. The coffins with the bodies of Peter I, who died on January 28, 1725, and his daughter Natalia, who died on March 4, were placed inside the under-construction church in a temporary wooden chapel. From 1727, the coffin with the body of Catherine I was also there. The three coffins were buried simultaneously on May 29, 1731, upon completion of construction. They were placed in a common crypt, topped with white alabaster tombstones. In 1732, Empress Anna Ioannovna ordered the removal of the existing sarcophagi in the cathedral for replacement. Throughout the 18th and 19th centuries, all emperors and empresses were buried in the cathedral, except Peter II and Ivan VI. The ashes of Peter III were transferred by order of Paul I from the Alexander Nevsky Monastery to the cathedral on December 5, 1796, and buried together with the remains of Catherine II.
In the 19th century, a "Funeral Commission" was established by decree to organize burials, headed by the highest court officials. The commission involved many famous architects and artists: D. Trezzini, M. G. Zemtsov, A. F. Vista, A. F. Kokorinov, V. Brenna, and Giacomo Quarenghi. Only Montferrand decorated the cathedral four times (for the funerals of Alexander I and Nicholas I, Empresses Elizabeth Alexeievna and Maria Feodorovna). The burial ceremony was accompanied by cannon shots from the fortress and the ringing of city church bells. Members of the Synod, led by the Metropolitan of St. Petersburg, greeted the funeral procession at the western doors of the cathedral. The catafalque was usually placed in the central nave under a canopy rising to the ceiling. Symbols of state power were placed before the coffin of the emperor or empress.
From 1831, the cathedral also buried grand dukes, grand duchesses, and princesses, with a more modest ceremony. The grave was a crypt (2.5 meters deep, 2.4 meters long, 1.2 meters wide), its walls and bottom lined with limestone slabs. The heart and internal organs were placed separately before the main burial. The coffin in a copper ark was locked, and after burial, it was covered with sand. The grave was covered with a stone slab with a tombstone: from the 1770s to the 1840s, sarcophagi of gray Ruskeala (Karelian) marble without decorations. In March 1865, Alexander II ordered the replacement of the dilapidated tombstones. The workshop of G. A. Balushkin, following the design of the architect of the Imperial Court Ministry A. A. Pouaro, who supervised the cathedral at that time, and engineer G. E. Pauker, produced 15 new tombs by January 1867 made of white Italian (Carrara) marble. In June 1867, double-headed eagles cast in bronze and gilded, as well as crosses, were attached to the corners of the sarcophagi. Bronze plaques with texts composed by historian Ustryalov were fixed on the iron grilles surrounding the sarcophagi and on the cathedral walls. The 15 tombs (hollow boxes assembled in the church from 5 marble slabs) were made by merchant of the 2nd guild G. A. Balushkin. Subsequently, most tombstones (a total of 30) were created following this model.
In 1887, Alexander III wished to replace the tombs of Alexander II and his wife, Maria Alexandrovna, with new ones. Tombstones made of gray-green Altai jasper and pink Ural rhodonite weighing 5.1 tons and 6.7 tons with carved crosses and ornaments were made at the Peterhof cutting factory. In 1907-1909, new marble slabs with bronze crosses and inscriptions were installed over the graves of Peter I’s sister Maria Alexeevna, Tsarevich Alexei, and his wife, located under the bell tower. By 1917, the church contained 41 burials. The tomb of Emperor Paul I was especially revered in the early 20th century. Tombstones were decorated with numerous relics: icons in precious settings with lamps, silver wreaths, banners, commemorative medals, Easter eggs, etc. For example, on Peter I’s tomb stood an icon of the Apostle Peter by Simon Ushakov in a golden setting. On Alexander II’s tomb were 6 lamps, 3 candlesticks, 21 icons, 10 crosses, a Gospel, 8 medals, 5 Easter eggs, 2 banners—trophies of the Russo-Turkish War, 165 silver wreaths; on Alexander III’s tomb—25 lamps, 54 icons, 674 wreaths.
In the cathedral, as a memorial of Russian military glory, trophies of the Russian Army were kept: Swedish banners taken at Poltava and during other battles of the Northern War (now in the Hermitage), Polish, Persian, French standards, kettledrums, and maces. The admiralty Turkish flag, taken in 1770 during the Battle of Chesma, was personally laid by Empress Catherine II on the tomb of the founder of the Russian fleet—Peter I—two years later (the decoration of the banners was done by Auguste Montferrand in 1855).
Sources:
https://www.pravenc.ru/text/2580504.html