In 1988, Janda became a member of the team of Teatr Powszechny (Popular Theatre) in Warsaw. Lech Sokół wrote about her debut role in Strindberg's Miss Julie directed by Wajda:
In essence, the Miss Julie we observe on stage is a figure who reveals the doubts and hysteria she has previously hidden from those around her, traits that consistently lead her towards tragedy, and ultimately to suicide. This role is indubitably difficult, but also immensely fascinating.
During her tenure at the Powszechny, the actress appeared in a number of immensely successful starring roles. After Miss Julie, the actress played the title role in Euripides' Medea directed by Zygmunt Hübner (1988). Tomasz Kubikowski wrote:
She is practically the only complete character on stage, preserving her autonomy relative to the compositional arrangements of the director. It is upon her that the entire conflict is based and she who commands it.
Maciej Nowak added,
Hübner and Janda have succeeded at a daunting task, namely, that of constructing a deep, none too psychologically simple motivation for the actions of the mythological heroine. Their construction has turned out to be shockingly contemporary.
In 1990, the actress featured in yet another stage production directed by Wajda, William Gibson's Dwoje na huśtawce (Two for the Seesaw), in which she played Giselle Mosca. Wojciech Dudzik reviewed the play for Rzeczpospolita daily, writing
Wajda has found excellent performers in Krystyna Janda and Piotr Machalica. Janda plays a certain nervousness (but without her sometimes irritating mannerisms from 'Man of Marble'), and she proves capable of being lyrical at times. Underlying her singular primitivism is a longing for a different, better life, for which she struggles and which she simultaneously fears.
Following that appearance, and also in 1990, Janda teamed up with director, Maciej Wojtyszko, to tackle Willy Russell's one-woman show, Shirley Valentine. The production proved a tremendous success. Janda, who could never be denied emotional authenticity on stage or immense respect from her audience, found her range with the role of Shirley. After the premiere, critic Jacek Sieradzki wrote in the weekly Polityka,
The actress has strongly worked through Małgorzata Semil's translation, making it fit her lips ideally in its entire commonness, colloquial tones, brevity and vulgarisms. She has invested tremendous energy in an effort to bring out Shirley and make her a sympathetic character for viewers. At times, this comes across as catering to the public, as if the purpose was to elicit chuckles of approval and comments like 'damn, she's babbling away'. However, this was only up to a point. Confident of the sympathy of her audience, the actress complicated the image of her heroine, revealing her insecurities and complexes concealed beneath the boastful talk. (...) The performance I saw ended with a standing ovation. Apparently, Krystyna Janda is thanked by her audiences in this manner evening after evening - for her performance and for the joy of hope she provides.
Janda continues to perform this one-woman show to the present day.
After Shirley Valentine, Janda continued to take on starring roles, playing the lead parts in both contemporary and classic plays. In 1992, she portrayed Margaret in Tennessee Williams' Kotka na rozpalonym blaszanym dachu (Cat on a Hot Tin Roof) directed by Andrzej Rozhin (1992), appearing alongside Piotr Machalica and Henryk Machalica. Natalia Adaszyńska wrote for Teatr monthly:
Everything seems to indicate that the actors were chosen for their names to ensure the production's success, because this staging has no other merits. (...) In watching the scenes, one has the impression that the director has done nothing to challenge the actors, allowing them instead to be guided by their experience, intuition, if not merely by their routine. This is especially true of Krystyna Janda's performance. Those who have seen her in 'Shirley Valentine' or 'Educating Rita' are sure to recognize the character choices they know from those productions. In this case as well, the actress builds the character of Margaret from sharp gestures, characteristic breaks of the voice, a nervousness and trembling of the hands that accompanies the lighting of cigarettes.
Janda then appeared as Andrea Salas in Ariel Dorfman's Śmierć i dziewczyna (Death and the Maiden) directed by Jerzy Skolimowski (Studio Theatre in Warsaw, 1992), and as the title character in the one-woman play, Kobieta zawiedziona (A Woman Scorned) based on the writings of Simone de Beauvoir and directed by Magda Umer (1994), and as Lady Macbeth in Shakespeare's Macbeth staged by Mariusz Treliński (1996). In the latter, according to Jacek Cieślak, she
(...) played Lady Macbeth in a sentimental, teary style reminiscent of South American television soap operas.
She also portrayed Maria Callas in Terence McNally's Maria Callas – lekcja śpiewu / Maria Callas: a Singing Lesson, directed by Andrzej Domalik (1997). Aleksandra Rembowska wrote in Teatr monthly:
For two and half hours, Janda-Callas (perfectly made up and costumed) completely commands not only her own feelings (...), but also those of her audience, whom she treats as the observers of a singing lesson, including them in the exercises and dominating them entirely. She proves capable of inducing the audience to react as she wishes, at the moment of her choosing. (...) It is important that Janda portrays this primadonna with noble restraint, largely abandoning the tone of many of her previous roles, her characteristic spontaneity, even the over-excitement that rendered so recognizable her 'scorned women'.
Janda also appeared as the lead in Jean Racine's Phaedre directed by Laco Adamik (1998).
Her many film roles of the 1990s and beyond included such noteworthy performances as Magda in Maciej Ślesicki's Tato (Dad, 1995), and Ewa in Robert Gliński's Matka swojej matki (Her Mother's Mother, 1996). She also appeared in Krzysztof Zanussi's Życie jako śmiertelna choroba przenoszona drogą płciową (Life as a Fatal Sexually Transmitted Disease, 2000), Wojciech Marczewski's Weiser, based on the renowned book by Paweł Huelle (2000), and in Filip Bajon's Przedwiośnie (The Spring to Come), a screen adaptation of Stefan Żeromski's classic novel, Przedwiośnie (Early Spring, 2000).
The 1990s marked the beginning of Janda's career as both a film and theatre director. She directed the film Pestka (Core [aka The Pip]), based on the book by Anka Kowalska (1995), and a number of productions for Polish Television Theatre, including Henrik Ibsen's Hedda Gabler (1995), Pierre Corneille's El Cid (1996), Honore Balzac's Fizjologia małżeństwa (The Physiology of Marriage, 1999), Dario Fo's Związek otwarty (The Open Couple, 2000), in which she teamed up with Marek Kondrat to portray an intensely comedic married couple, as well as Michał Bałucki's Klub kawalerów (Bachelors' Club, 2001), and Esther Vilar's Zazdrość (Jealousy, 2001). At the Powszechny Theatre, her directing projects during this period included Ernest Bryll and Katarzyna Gaertner's Na szkle malowane (Painted on Glass, 1993), and Witkacy's Panna Tutli-Putli (Miss Tootli-Pootli, 1997).
Janda also worked with director Zbigniew Brzoza. She played Karla in his production of Ingmar Villqist's Noc Helvera (Helver's Night at the Powszechny Theatre, 2000) and then surprised audiences with her performance as the titular character in Lee Halls' Mała Steinberg (Spoonface Steinberg at Warsaw's Studio Theatre, 2001). In the latter production she took on the challenging role of portraying a character afflicted by illness and disabilities. Roman Pawłowski wrote in the daily Gazeta Wyborcza:
The acting skills of Janda, who on stage transforms from a beautiful woman into a stooping, closed child, places the reviewer in a less than comfortable position. Am I supposed to assess the degree to which the actress has convincingly portrayed actual illness? Should I criticize her for not groaning often enough or for moving about too easily? It would be better for the play if Janda had rejected this naturalism, which instead of helping audiences in experiencing and understanding the true story of this girl conceals this story beneath theatrical form. Because in theatre, illness portrayed by healthy actors is only form, pretense. (...) While the theatrical form of 'Spoonface Steinberg' at the Studio is controversial, the entire concept of staging a play of this nature is unquestionable. In a country where disabilities exclude people from society, it can never be repeated too often that people with disabilities are people too. Janda once more provides proof of artistic and civic daring - after playing Karla, the guardian of a boy with disabilities in Ingmar Villqist's 'Helver's Night', she has this time chosen another social drama, one which reveals the rich spiritual and emotional life of a child afflicted by illness. So when Janda came out for her bows, I stood with the other audience members, because this is an actress who deserves recognition for her courage and her engagement on behalf of the weak and rejected.
In January 2003, Janda celebrated the twenty-fifth anniversary of her acting career. To mark the occasion, Warsaw's Studio Theatre mounted a production of Chekhov's The Seagull directed by Zbigniew Brzoza, and featuring Janda as Irena Arkadina. As has been the case many times previously for this actress, the premiere ended in a tumultuous standing ovation