Designed by master mason Don Meir (Mayr) Abdeil,[4] it was built in 1357 in the Mudéjar or Moorish style as an annex of the palace of Samuel HaLevi, treasurer to King Peter of Castile.

[6] His family had served the ruling Castilian House of Burgundy for several generations and included kabbalists and Torah scholars such as Meir and Todros ben Joseph Abulafia.

[6] Some scholars suggest that Peter of Castile assented to the synagogue's construction as a token of appreciation for Samuel’s service as counselor and treasurer to the king.

As to why the construction of this synagogue would have been allowed remains debated, but scholars reason that it was due to Samuel's relationship with King Peter of Castile, or the fact that it was a private home.

In 1884, Arturo Mélida y Alinari replaced Francisco Isidori as the head architect of the project, focusing mainly on the roof, façade, and reinforcements.

The building fell back into disrepair before it became part of the El Greco Museum in 1911, when a new large-scale phase of restorations began.

Adding a library to the lower part of the gallery, which has since become an important center for Hebrew studies, entailed the demolition of large portions of the façade.

[7] With the apparent approval of the king, Samuel defied the laws that required synagogues to be smaller and lower than churches and plain when it came to decoration.

The gallery is located along the southern wall, having five broad openings looking down towards the ark of the Torah, called the hekhal by Sefardic Jews.

In contrast with the highly ornamented interior, the synagogue's exterior was built of brick and stone and was plain and largely unadorned.

The mixed stone and brick exterior walls are simple, with an aljima window (a pair of horseshoe arches) over the entry door.

[18] Its façade was and remains a prime example of mudéjar architecture in al-Andalus which symbolizes the social status, power, and influence of Samuel ha-Levi.

Around the same time as the construction of the synagogue and the Alhambra by Muhammad V, Peter of Castile restored the Alcazar of Sevilla, a historic Almohad fortification with Nasrid architectural and mudéjar design elements.

[18] Islam architecture and aesthetic mixed with the Castilian coat of arms are significant in that it indicates a connivance from Ha-Levi towards the dominating religions.

[11] For example one of these reads: Bi'l ni'mah wa-bi'l quwah wa bo'l karamah, roughly translated, "by (or in) grace, power, magnanimity (or, alternatively, generosity or happiness), salvation".

[19] The Hebrew inscriptions surrounding the coat of arms, reads as follows in English:[11] "Of the graces of the Lord let us sing and of the works of the Lord according to what he has bestowed on us and hath done great things with us...instituting judges and ministers to save his people from the hand of Enemies and oppressors And there is no King in Israel, he hath not left us without a Redeemer He is the bulwark tower, which since the day of the exile of Ariel None like him has risen in Israel For the Name and the glory and the praise Known is his name in Israel since the day he dwelt on his land and stood before Kings To him who stands in the breach And seeks the good of his people Head of the exile of Ariel, The select of the leaders.

Due to its deteriorating state, the exact date is not clear; however, scholars are able to determine the year by using Hebrew words that double as numbers in the language.

It references Bezalel and the biblical story in which he is chosen to build the Tabernacle, creating an allusion to haLevi himself:[19] And its atriums for those attentive to the perfect Law/and its seated places for those who sit in His shadow/of such a type that those who see it must almost say: The design of this [temple]/ is like the design of the work by Bezalel/Walk, nations, and enter through its doors/And look for God, since like the house of God it is, like Bethel" [19]In the prayer room, on top of the four walls the ceiling, just below the ceiling we find the following inscription:[11] "See the sanctuary now consecrated in Israel And the house which was built by Samuel with a pulpit of wood for reading the law With its scrolls and its crowns all for God And its lavers and lamps to illuminate And its windows like the windows of Ariel" Some experts believe the inscriptions also refer to another renowned Samuel, a Levite named Samuel ibn Naghrela (993-1056), a significant Jewish leader throughout the Middle Ages, both Samuels were proud of their Levitic ancestry.

The symbolic placement of stucco mixed with the inscriptions (discussed above) is reminiscent of the Alhambra since Samuel intended that the spectator could read the architecture and art like a book, as is seen in alcázares and mosques in al-Andalus.