Considering Nacho Fresneda being cast as a soldier of the Tercios being recruited for a secret government mission (and getting mostly positive reviews), Alonso being jokingly called "Captain Alatriste" several times and getting the book to read it, the second episode including scenes in a dark Siglo de Oro tavern (and the first having a brief scene in an equally illy-lit 1500s Madrid street), and Velázquez protesting in the third episode that his paintings are being restored the wrong way and now look "like a Spanish TV series", the first season is basically a Strongly Worded Letter to Telecinco about how to make a betterAlatristeTV adaptation than they did.
While it might be unintentional, the opening of the series evokes strongly the Russian animation-esque visual style of Puella Magi Madoka Magica, an anime series whose premise orbits similarly around Time Travel. The plot of both series also shares a dark-haired, no-nonsense female character bent on changing history for the better (Lola Mendieta in El Ministerio and Homura Akemi in Madoka) who has an ambivalent relationship with a sweet, naive female lead entasked with protecting her world (Amelia Folk and Madoka Kaname, respectively).
Episode 1 ("El tiempo es el que es")
Julián compares Thibaud's plan to kill El Empecinado before he organizes the guerrilla war against the Napoleonic occupation to the plot of Terminator. There is a Call-Back to this in a pre-Season 2 promo (Alonso, Amelia and Velázquez watch Terminator) and another in Episode 9.
Julián adopts the alias "Curro Jiménez" as an Actor Allusion to Rodolfo Sancho's father, the late Sancho Gracia, who played the titular bandolero. The circumstances (an impromptu decision while in a tavern from around the time the reference work was set in) is also reminiscent of Back to the Future.
Episode 2 ("Tiempo de gloria")
Lope de Vega recites Orlando Furioso while he handily beats a man over a woman.
Julián recites a stanza of Maneras de Vivir, from '80s rock band Leño.
Amelia reads Lope's La Dama Boba ("The Foolish Lady") at the end of the episode. Her own actions in the episode are more in line with the book's plot that she realizes.
Groundhog Day is namechecked, as the gate they have to use runs on similar rules.
Several to the Spanish series Isabel, which is from the same crew:
Actress Michelle Jenner reprising her role as the Queen of Spain and Julián, whose actor played his husband in the series, remarking that she seems familiar.
Cisneros, also played by the same actor as in Isabel, looks to Julián when Isabel asks if her husband has been informed.
The Isabel motiff plays during the scene where Levi heals young Isabel's hand.
Episode 5 ("Cualquier tiempo pasado")
Since both series are produced and aired by the same channel, rumor was that, after the nod to Isabel, some Cuéntame Cómo Pasó character would make a cameo. It turns out that, unlike Isabel, Cuéntame is a fictional series in-universe and Julián jokingly refers to the 1981 safe house as "the home of the Alcántaras".
More obscurely, the jacket that Julián wears in this mission and that he complains makes him look like his father, was worn first by Cuéntame's main character, Carlos Alcántara.
Velázquez meets with Picasso, who states that Velázquez is the greatest Spanish painter ever, much like it happened with Van Gogh in Doctor Who's episode "Vincent and the Doctor".
The character Paul Walcott's name is probably a reference to the villain Patrick Walcott from Águila Roja, also produced by RTVE.
Dividing and showing various events in vignettes, suspiciously similar to 24.
Episode 8 ("La leyenda del tiempo")
Silvia infatuated with Julián. Silvia is Amelia's granddaughter and has a big chance that she might be related to Julián too. This has been seen before.
Julián reads (and quotes) Lorca's Poet in New York.
The play at the Student Residence is a version of Zorrilla's Don Juan Tenorio. Alonso is inspired by the play to make revenge on his wife's second husband for mistreating her.
TV host JordiHurtado is revealed to work for the Ministry and his current mission is going to the past to shoot more programs of his show, Saber y Ganar.
Episode 9 ("Tiempo de leyenda")
Obviously, El Cantar de Mío Cid. Especifically, how the Cantar doesn't always align with the real man's life, despite being the source of his image in popular culture.
Driving the point home, Rogelio went to the Middle Ages to get documentation for the 1961 film El Cid, the reason most non-Spaniards are familiar with El Cid today.
Spínola, in a fight, shouts "Yippie-kai-yay, hideputas", medieval Spanish version of a certain action film hero's Catchphrase. Also an Actor Allusion given that he is played by Ramón Langa, who voices the actor of said action film hero in Spain.
The ending is an elipsed sortie against a CGI besieging army many times over, like the climatic scene in The Return of the King.
David Sainz from webseries Malviviendo has a cameo as a Ministry agent and gets to drop his Catchphrase "that's flow".
Episode 10 ("El tiempo en sus manos")
To Frequency, with time-travel shenanigans being used to capture a murderer and things vanishing after history is changed.
New Ministry agent Jesús Méndez's nickname is Pacino because he looks like Al Pacino in Serpico. Also, when he says Al Pacino is the best actor in the world, Salvador promptly mentions that he prefers Laurence Olivier.
The 1981 newspaper reporting about the disappearance of Pacino is El Caso. This is a nod to another TVE series, which premiered three weeks after this episode was aired, set in the editorial office of said newspaper. In fact, each of the series' Twitter accounts tend to refer to each other pretty often.
Once again, to "Vincent and the Doctor", with Miguel de Cervantes as Vincent, visit to the future to learn about his role in history included.
To Don Quixote, obviously, since getting the book published is the mission of the episode (and Alonso takes it to the past to read it), but the crew shows their work by referencing parts of Don Quixote that are not well known, such as The Captive's Tale and Grisostomo's Desperate Song. Several other works by Cervantes and Lope de Vega are mentioned.
During Miguel de Cervantes' visit to the future, there are images of different adaptations of Don Quixote.
An Older and Wiser Lope de Vega reflects on his past as a young Spanish Armada soldier and Chick Magnet, rekindling with a Spanish lady that makes him feel rejuvenated, and working with two "Englishmen" in hopes of getting his plays performed in London, without realizing that they are actually plotting against him and his country? All done in Ruled Britannia. Lope being surprised to hear of La Dama Boba years ahead of time and writing the title down to maybe make a play about it is a Historical In-Joke but also another possible nod to Ruled Britannia, where Lope wrote that book decades before he did in real life.
While in Shakespearean (well, Cervantine) times, the villainous Walcott poses as an English nobleman: Lord York.
The two Americans teleport in a way very similar to Star Trek.
Sonia, desperately trying to find anything that will prove she has not traveled back in time, points to a beggar, saying she has seen him in Isabel and Águila Roja. Also an Actor Allusion/Casting Gag, because yep, he had been in those.
Since the main plot of the episode revolves around Alfred Hitchcock's visit to the San Sebastián Film Festival, the episode is pretty much a tribute to him, chock-full of references to his filmography.
The beginning in the tavern ends up with a shooting between Nazis and rebels, the waiter dying, a well-dressed woman talking with a German officer and ending up being taken. This was seen once upon a time in Nazi occupied France.
Pacino mentions Ian Fleming, James Bond and Get Smart... as well as Anacleto, Agente Secreto, a Spanish comic book that parodies James Bond and Get Smart.
Episode 24 ("Tiempo de hechizos")
Pacino telling Bécquer the story of his shipwreck is actually the plot of Titanic (1997).
Goya telling Velázquez, who is a great admirer of his work, to "Go yourself to the shit!"note In Spanish, "¡Váyase usted a la mierda! ¡A la mierda!" is a reference to actor Fernando Fernán Gómez's angry response to a fan.
Episode 27 ("Tiempo de esclavos")
After finding a clue in the suspect's bedroom in the palace, Pacino says "Definitely these people have never watched Columbo".
Episode 29 ("Tiempo de conquista")
Pacino's disguise while in 1518 is identical to Captain Jack Sparrow's, and he moves in the jungle just like Jack.