In this work, an approach for a preference-based job-flow scheduling in Grid virtual organizations is proposed and studied. Virtual organizations provide uniform rules of the resources sharing and consumption and should respect individual and common preferences of its stakeholders: users, resource providers and administrators. In most cases, a virtual organization’s stakeholders pursue contradictory market-based goals, which may be expressed in terms of time and cost. Still, mutually beneficial job-flow scheduling scenarios are possible in such multi-agent computing environments when the different optimization criteria are coordinated. For this purpose we consider different resources allocation heuristics and scenarios based on a simple linear combination of global (group) and private (user) job scheduling criteria. We study backfilling-based job queue scheduling procedure with a secondary preference-based optimization performed only on the resources allocation step. This approach allows us to respect backfilling-based jobs execution priorities together with more specific individual jobs criteria, including total execution cost or time minimization.