In addition to the over seventy-five works she has made for her Company, Jenkins' choreographic work has been commissioned by the New Dance Ensemble in Minneapolis, the Repertory Dance Theatre in Salt Lake City, the Oakland Ballet, the Cullberg Ballet of Sweden and Ginko, a modern dance company in Tokyo, Japan. She has received commissions from the Clarice Smith Center for the Performing Arts, Yerba Buena Center for the Arts (YBCA), National Dance Project, the Krannert Center for the Performing Arts, Arizona State University, the University of Arizona, and Columbia College in Chicago, as well as being a recipient of a National Dance Residency Project grant. She has set work on various college and university dance departments and has also embraced a commitment to training the professional dancer. Over the last forty years, she has taught at major universities and colleges in this country and abroad.

Highlights of Jenkins' activities in the last ten years have included a residency in Kolkata, India (2003) to create a new dance at the Ananda Shankar Center for Performing Arts, the premiere of a new site-specific work, Danger Orange (2004) in San Francisco, a three-week teaching residency in Hong Kong, Guangzhou and Beijing, China (2004). In 2005, she created running with the land (2005) for the opening of the new de Young Museum in the Barbro Osher Sculpture Garden, commissioned by the Barbro Osher Pro Suecia Foundation. That same year, Jenkins and her Company completed a four-week rehearsal and performance residency in India toward the creation of A Slipping Glimpse, an evening-length work that premiered in 2006. For the 75th anniversary of the San Francisco Ballet in 2008, Margaret Jenkins was commissioned to create Thread, a new work for which long-time collaborator, Paul Dresher, created a new musical score.

In 2007, Jenkins and her Company performed in a poetry and dance festival in Tokyo, Japan, conducted a five-city domestic tour of A Slipping Glimpse including performances in India, and presented the initial segment of Other Suns, the first part of new trilogy of work inspired by her 2004 workshops in China, The complete Other Suns trilogy had its world premiere in September 2009 at YBCA, followed by a highly successful five-week tour in the U.S and a tour of China. 2011 brought the long-awaited premiere of Light Moves, Jenkins' collaboration with multi-media artist Naomie Kremer, which also toured the US.  For her 40th anniversary in 2013, she will create Times Bones, based on gathering the scattered bones from her older work, as well as Barrier Winds in collaboration with her Company and dancers from Israel.

As an organizer and enthusiast for dance, Jenkins facilitated a showcase for presenters to be introduced to the work of Swedish choreographers in Stockholm, some of whom subsequently came to San Francisco and other US venues. She served on the steering committee for the 2002 International Women's Day Conference in San Francisco, and as Artistic Consultant to Dance About, a dance facility at the UC Berkeley Extension in San Francisco. She was a founding member of the Bay Area Dance Coalition and of Dance/USA, serving on its first Board of Directors. She is currently on the board of directors of Yerba Buena Center for the Arts in San Francisco.  She remains an active participant on panels across the United States.

Jenkins is committed to an art of inquiry and to advance the health and future of the field of dance through a variety of projects. In 2004 Jenkins and her Company launched Choreographers in Mentorship Exchange (CHIME). The notion behind this year-long artist mentorship program is to foster creative exchange and long-term relationships between emerging and established choreographers, and to create an arena for continuing education for choreography outside of the academic environment. Coinciding with the commencement of CHIME, she opened her new studio, the Margaret Jenkins Dance Lab, in the South of Market area of San Francisco, her seventh working space in San Francisco, since 1970. Since its inception, CHIME has expanded to include CHIME in Southern California, which engages artists in Los Angeles, and CHIME Across Borders, which brings internationally renowned masters of dance to San Francisco to work with locally established choreographers for sustained mentorship work over the course of one year. The first three Borders choreographers were David Gordon, Ralph Lemon and Elizabeth Streb.

Jenkins has also helped to structure and implement Choreographers in Action (CIA), a unique gathering of Bay Area choreographers who, in combination and collaboration, posit solutions to the myriad of issues that surround the working artist. In addition, Jenkins was one of the founding members of the Center for Creative Research based in New York, which is a collection of eleven senior choreographers who have come together under the leadership of Sam Miller to create artistic research residencies within universities.