The manuscript P-Pm MM-42 (olim Ms. 1577), with organ tablatures (same system used by Venegas de Henestrosa, Hernando de Cabezón and Correa de Araujo), contains the only four works known by this organist/composer: two are titled Obra and the other two Registro. According to Preciado (1999-2002), p. 715, the obras are "llenos para órgano" and the registros are "registros partidos de mano derecha (de uno y dos tiples, espectivamente)"; the four works are like tientos. He points out: "Es notable la Obra de 5º tono, porque en su segunda mitad introduce el autor un motivo de jota riojana, que le confiere un aire de fiesta popular. Antonio Brocarte aclara el estilo organístico español de su tiempo, haciéndolo menos farragoso y más transparente".

As pointed out by José López-Calo and Cristina Diego Pacheco, documents related to the brothers Alonso, Pedro and Rodrigo Ordóñez often do not mention the first name, and thus it is difficult sometimes to ascertain their identity. In E-V 05 there are four polyphonic works attributed to Alonso Ordóñez and one to "Rº Ordóñez"; although the initial in the latter ascription has been interpreted as "Racionero" (to refer to Alonso Ordóñez), it is most likely that it refers to Rodrigo Ordóñez. There are no known works attributed to Pedro Ordóñez.

López-Calo mentions many possible locations that can or could be related to Rodrigo Ordóñez.