He trained with Girolamo Muziano, and under this master, he helped complete a flurry of decoration that was added to the Cathedral of Orvieto in the 1560s. Almost all the remaining work in Orvieto is now in the Museo del Duomo.
Nebbia and Muziano became active in many of the premier projects in late 16th-century Rome. Nebbia and Muziano's other assistant, Giovanni Guerra, decorated the Gregorian Chapel in the St Peter's Basilica during the administration of Gregory XIII (1572–1585). Other Mannerist painters that were involved in this enterprise were Taddeo and Federico Zuccari, Niccolò Circignani, and Hendrick van den Broeck (known as Arrigo Fiammingo).
Fresco decorations in Palazzo Simonelli in Torre San Severo have been attributed to Nebbia. In 1576, he painted a Resurrection of Lazarus for the Church of Santa Maria dei Servi in Pieve.
During the administration of Pope Sixtus V (1585–1590), Nebbia and Guerra together managed the two major fresco decorations commissioned by the papacy: the construction and decoration of the Capella Sistina at Santa Maria Maggiore and the refurbishment of the Scala Santa and the chapel of St. Lawrence found adjacent to the Lateran palace and San Giovanni in Laterano.
The Sistine chapel of Santa Maria Maggiore was meant to be a burial chapel for pope Sixtus, and constructed over the supposed presepe relic, and should not to be confused with the more famous Vatican counterpart, the Sistine chapel.
The Scala Santa project involved an amalgam of structures, it comprises five parallel staircases leading to a common corridor, opening up to chapels, the central one of which was the private papal chapel of St. Laurence or Sancta Sanctorum of the gothic Lateran Palace, and held numeorous relics, including the icon of Santissimi Salvatore Acheiropoieton (not painted by human hands). The staircases were said to have been from the palace of Pilate in Jerusalem.
In the project at Santa Maria Maggiore starting in 1586, Baglione traditionally lists for ten painters who were active in the fresco decoration as Hendrick van den Broek, Angelo from Orvieto, Ercolino from Bologna, Salvatore Fontana, Lattanzio Mainardi, Ferdinando Sermei, Giacomo Stella, Giovanni Battista Pozzo, and Paris Nogari. The decoration for the church and a chapel which held the relic of the Nativity (the original Presepe or manger crib) shows scenes of the life of the Virgin. For the project at the Scala Santa, an overlapping crew of artists was also employed to decorate frescoes including Giovanni Baglione himself, Stella, G.B. Pozzo, Nogari, as well as Prospero Orsi, Ferraù Fenzoni, Paul Bril, Paulo Guidotti, Giovanni Battista Ricci, Cesaro Torelli, Antonio Vivarini, Andrea Lilio, Cesare & Vicenzo Conti Baldassare Croce, Ventura Salimbeni, and Antonio Scalvati. Numerous preliminary drawings by Nebbia exist for these frescoes.
Nebbia helped paint galleries in Vatican libraries including the ceilings of map gallery. During Clement VIII he designed pendentive mosaics for Matthew and Mark for St. Peter's Basilica. He painted a Crucifixion for Borghese chapel in Trinità dei Monti. He painted a resurrection for San Giacomo degli Spagnoli. He painted a Coronation of the Virgin for Santa Maria dei Monti.
Along with Il Bertoia, Federico Zuccari and others, he helped paint the frescoes on the wall of the Oratorio del Gonfalone in Rome. He also contributed to the decoration of the Oratory of Santissimo Crocifisso.
In 1603-1604, he moved to Milan where he worked for Federico Borromeo painting a series of frescoes on the life of the Blessed Carlo Borromeo for various sites, including the Collegio Borromeo in Pavia, the collegiata di Arona, and the Palazzo Borromeo on Isola Bella.
- Eitel Porter, Rhoda (2009). Der Zeichner und Maler Cesare Nebbia 1536-1614: Mit einem Katalog der Zeichnungen (Römische Studien der Bibliotheca Hertziana). Munich, Hirmer Verlag.
- Eitel Porter, Rhoda; Alberto Satolli (July, 1994). "Cesare Nebbia's Work for the Palazzo Simoncelli: Drawings and Frescoes". Burlington Magazine (136): pp. 433–438.
- Eitel-Porter, Rhoda (1997). "Artistic Co-Operation in Late Sixteenth-Century Rome: The Sistine Chapel in S. Maria Maggiore and the Scala Santa". The Burlington Magazine: pp. 452–462.
- Freedberg, Sydney J. (1993). In Pelican History of Art. Painting in Italy, 1500-1600. Penguin Books. p. 647.
- Baglione, Giovanni (1641). In Giovanni Battista Passari. Le Vite de’ Pittori, Scultori, Architetti, ed Intagliatori dal Pontificato di Gregorio XII del 1572. fino a’ tempi de Papa Urbano VIII. nel 1642. 1731 edition (Naples); Digitized by Googlebooks. pp. page 110.
- Baglione, GB. p. 110-111.
- Rhoda Eitel-Porter, p. 452