Six one-meter test units excavated in the center of the ballast mound revealed well-preserved and articulated lower hull remains that are quite similar to the architecture of other 16th-century shipwrecks that have been studied in Europe and America. These features include an expanded keelson (the inner spine of the ship) on which to step the mainmast, with mortise and chock to house the foot of the mast; two pump wells to house the shafts of the ship’s bilge pumps; and a series of perpendicular buttresses to laterally support the mast step in the hull. A test trench excavated perpendicular to the keelson on the port side of the ship revealed that the ribs and hull planks had been broken, probably by severe pounding of the ship’s bottom on the sand bar. These clues suggested that the ship had struck the shallow bar in a violent storm, sometime in the 16th century, could not be refloated, and eventually was abandoned.

During excavations of the mainmast step, a small cross was discovered gouged into the base of the mainmast mortise. While the meaning of this mark is unclear, since it has not been observed or recorded on other shipwrecks, it may possibly have had religious significance, much like the secular practice of depositing a coin in the mast step for good luck. This mark also is located at the ship's point of maximum breadth.  

At the base of the mainmast mortise was a small wooden mast chock to wedge the foot of the spar into place. There is also a drilled hole which may have been intended for an iron bolt to fasten the keelson to the keel, or perhaps was intended as a drain hole to allow seawater to gravitate into the bilge, rather than soften and rot the heel of the mainmast.

A ship's pumps are the most important safety feature on a seagoing vessel. The Emanuel Point Ship employed two pumps, one on either side of the keel at the lowest part of the hull where water collected in the bilges. Carved into the sides of the keelson, the pump wells were fitted with pump shafts fashioned from hollowed-out tree trunks in which a piston and rod operated to expel water. The first daylight watch began with pumping of the bilges; if the water was foul and dark, the crew was glad—if clear and green, they had to worry.

Deep in the bilge, among scraps of wood and other carpenters' debris just abaft the port sump, a curious and unique object was discovered: the small carved silhouette of a ship in the shape of a typical 16th-century Spanish galleon. The location of this small carving, beneath ballast and bilge sediments, suggests that it probably was deposited in the ship at the time of its construction, perhaps inadvertently left behind by an apprentice shipwright.

Features of the small carving found on the Emanuel Point Ship, such as the heavy beak at the bow, and high fore-and sterncastles, are remarkably similar to those of a Spanish galleon model dated 1540, which is in the Museo Naval (Naval Museum) in Madrid. Although the model is much larger than the carving, the two are shown here to the same scale for comparison.

Eight fragments of leather were recovered during excavation of the main mast step. The three largest pieces are the remains of shoes. One may have belonged to a woman's or girl's platform shoe, known as a "chapin," of typical Spanish style. Another is from a shoe that appears to have been resoled, judging by a straight cut in the leather. The third shoe fragment is from a larger shoe or boot; wear marks suggest that it was worn on the left foot.

Hundreds of olive pits were found in the midships area of the lower hull intermixed with broken pieces of ceramic storage containers. The pits are of various shapes and sizes, suggesting that several kinds were present on the ship. A traditional Spanish food item, olives were transported at sea in botijas, or olive jars, as was olive oil, wine, vinegar, and other foodstuffs.

Animal bones, the remains of ship's provisions eaten by the crew and passengers, show cut marks made by butchering and evidence of rodent gnawing. Mammal bones include cow and pig, but chicken and fish bones also were found in the shipwreck. None of the fish bones exhibit cut marks or rodent gnawing; they probably belonged to local inhabitants of the bay that lived and died around the wrecksite.

This organic deposit was recovered from the midships excavation near the port pump well. It contained fragments of stowaway insects that lived at one time aboard the ship. Entomologists have identified wings, thoracic segments, and egg cases of the American cockroach (Periplaneta americana), and wing covers from the hide beetle (Dermestes maculatus). Despite its misleading name, the American cockroach is believed to have originated in tropical Africa and was transported to the Americas on slave ships sailing from the west coast of Africa. However, this evidence demonstrates that the American cockroach arrived in the Americas before the slave trade reached large proportions. The hide beetle is known to attack stored goods such as leather, books, tobacco, tea, and cotton. The presence of numerous beetles aboard the Emanuel Point Ship suggests that they may have been brought to the vessel with a cargo, possibly leather hides.

Hundreds of fragments of ceramic jars were found in the hull of the Emanuel Point Ship. Most of the sherds, such as this rim and shoulder piece, are from containers called olive jars. The Spanish Olive Jar was a common container for transporting olive oil, vinegar, wine, and other foodstuffs on colonial sailing ships. The containers were emptied and reused for subsequent shipments, and are therefore commonly found on Spanish shipwrecks of the period.

Storing liquids in ceramic jars can result in seepage, since the coarse, low-fired wares tend to absorb their contents. One method of solving this problem was to coat the interior of the vessel with a waterproof substance. Many olive jar sherds from the Emanuel Point Ship were found to be coated on the interior with two different kinds of sealant: a clay slip on some, and pine pitch on others.