Wooden sailing ships plying the South Atlantic and American waters needed some form of protection from shipworms that quickly ate through the hull planking below the waterline. One method of protection was to nail strips of lead to the hull to cover vulnerable areas, such as the seams between planks. During excavations at the stern of the Emanuel Point Ship, over 200 fragments of lead sheathing or patching were recovered. All have holes left by sheathing tacks, and a few have impressions of fabric, which backed the lead. Some of the fragments of lead appear to have been patching material to repair leaks. Sheets of lead were also found covering the arms of the rudder hinges, or gudgeons. 

The ship's rudder was found lying behind and to starboard of the sternpost. It appears to have fallen from the sternpost onto its port side sometime after the wrecking incident. The rudder is constructed from two planks of wood, edge-joined with at least three large wrought-iron drift pins. Three pintles, representing the male components of the rudder hinges, are still fastened to the rudder. The forward surface of the rudder is hollowed out at the location of each pintle to allow the pintles to hang in the gudgeons, which are the female counterparts attached to the sternpost.

Over 250 milliliters of liquid mercury, or quicksilver, were found in the stern of the Emanuel Point Ship. The heavy metal most likely had spilled from its container into the bilge during shipment. Quicksilver was used in mining to separate precious metals from base metals in crude ores. First shipped under royal monopoly to Mexico in quantity during the 1550s, mercury became a principal ingredient in the amalgamation of silver from its ore. The presence of mercury in the bilge of the Emanuel Point Ship suggests that, at one time, the vessel had carried a cargo which included quantities of quicksilver, which may have leaked from containers and gravitated into the bottom of the hold. Transport of mercury was a tricky business, since the metal oxidizes very quickly, resulting in corrosion of containers and resultant leakage, which is difficult to recover, especially at sea.

A small coin was found lying buried under a piece of lead sheathing behind the sternpost. Highly encrusted with corrosion products, the coin is in very poor and fragmentary condition. Once the concretion was removed, the coin and its encrustation still retained sufficient detail to be identified by experts as a billon blanca, minted between 1471 and 1474, possibly at the Cuenca mint during the reign of Henry IV (1454-1474) of Castille and León. The term billon (vellón) refers to coinage made from an alloy of silver heavily debased with copper. Blanca was the lowest denomination of coins minted during this medieval monarch's reign.

Similar blancas of this type were unearthed during excavations at La Isabela in the Dominican Republic, the first European settlement in the New World, which was founded by Christopher Columbus in 1494. A single blanca of Henry IV also was found at the Long Bay site on San Salvador Island in the Bahamas, which is argued to have been the first American landfall of Columbus in 1492. Discovery of this late medieval example of "small change" at the stern of the Emanuel Point Ship is surprising, since by the 1550s, this would have been an old coin of little negotiable value.

A large number of rodent bones were found in the stern of the ship. They represent the remains of at least twenty-one black rats (Rattus rattus); however, it is likely that the total population of rats on board was greater. Rats have been common stowaways on ships throughout time, and undoubtedly came to the New World from Europe with the very first explorers. This drawing shows the outlines of bones recovered during excavations.

A unique group of ceramics was collected in the stern section of the ship. Called negro grafitto sobre rojo pulido, the ceramics are postclassic Aztec wares from the Central Valley of Mexico. Two curious, molded effigy sherds, one with a downward grimacing mouth filled with outlined teeth and surrounding facial decoration, the other with a molded left eye and cheek with facial decorations, appear to be in the Aztec IV tradition of 16th-century postconquest native pottery. Similar ceramic containers are depicted on an Aztec codex found at the Bibiothèque Nationale in Paris. The codex apparently was a legal plea by four potters from Cuauhtitlán to the resident Spanish judge in 1564 for reimbursement, since their wares had not been paid for by the local mayor, who had ordered them made. On the codex, the potters illustrated in color the forms and numbers of ceramic pots in question, along with their value. Among the pottery are containers with molded faces of Spaniards and Africans. Wares of this type often were used for ceremonial consumption of pulque, a fermented Mexican beverage. Apparently the Cuauhtitlán potters stopped making these wares after a massive epidemic of plague occurred in 1576.

To date, no artillery pieces or firearms have been found at the wreck site. However, the recovery of a variety of cannonballs, or shot, provides clues to the types of ordnance that were most likely carried aboard the Emanuel Point Ship. Four types of shot have been recovered thus far: stone, composite lead/iron, lead, and iron. These examples of ammunition suggest that the Emanuel Point Ship had been armed with heavy, stone-throwing cannons, medium wrought-iron artillery, and smaller swivel guns.

Eleven stone cannon balls, or bolaños, were discovered at the stern of the ship. The balls appear to have been fashioned by hand from limestone, probably with the aid of a template to guide the process of chipping the surface of the stone to a sphere of uniform size. Stone shot were fired from various large guns called pedreros (stone-throwers), or bombardas (lombards), and some of smaller caliber. They required less powder than other heavier ammunition to achieve their target; upon impact, the limestone balls tended to shatter into sharp projectiles that helped to destroy rigging and injure people.

An iron breast plate was discovered lying near the rudder in the starboard stern area. Heavily encrusted, the plate is one of the few surviving examples of metal body armor to be found in the New World. The former Curator of Royal Armor for the Tower of London has examined the Emanuel Point breast plate, determining it to date to around 1510, probably of Northern Italian manufacture. The armor probably was worn by a foot soldier who was larger than the average fighting man of the times. It predates, by more than a century, any body armor of this type found in the Americas.

The medieval armor plate has deteriorated after centuries under water. X-rays have confirmed most of the original metal has turned to graphitized sludge inside the concretion. However, careful cleaning and consolidation of the artifact may help to preserve what is left so that it can be displayed in a stable condition. Cat scans conducted by the Sacred Heart Hospital in Pensacola, have helped to reconstruct the original details and curvatures of the plate, so that a replica can made by a modern armorer for display.