On a chilly early evening last autumn, a few months after the results of the latest round of European Research Council starting and consolidator grants had been announced, staff members from across all divisions of the University of Oxford filtered into a cosy room at Exeter College. There, past and recent recipients of ERC grants were welcomed by Andrew Hamilton, the vice-chancellor, who spoke enthusiastically and inspiringly about Oxford's commitment to research.

His words captured why it had been worth drafting lengthy applications, holding preparatory meetings, going through repeated evaluations by subject and sub-faculty groups, faculty boards, college committees and governing boards, preparing for a 10-minute presentation and a half-hour interview in Brussels carried out by an expert panel of 15 international peer reviewers, and then starting negotiations all over again when the good news arrived. But conversations with the grantees dampened the atmosphere somewhat.

Admittedly, I may have been disposed to pick up on what sounded out of tune. As a recent awardee, I was eager to learn from past grant holders how pre- and post-notification negotiations with their faculties on issues such as resourcing compared, how they managed the duties of a large project alongside their faculty and college commitments, how best to meet the ERC's expectations, and how their research was going. This curiosity was not for curiosity's sake, however; it was motivated by the problems I had encountered.

A tentative exploration at the reception confirmed that I was not alone: at least three other junior ERC awardees had been left with a bitter taste in their mouths.

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The first person I met was a second-year grant holder who described repeated minor but hurtful acts of sabotage by more senior colleagues in a small faculty, plus a lack of support in staffing matters. This reminded me of the odd comment I had received from one colleague more than a year earlier when I first pitched my intention to apply. Rather unusually, she was opposed to the idea of anyone applying for grants and suggested that things could get difficult for me should I go ahead.

Another academic at the reception noted the exclusive interest of another member of their faculty in comparing the financial benefits of the ERC with other schemes. The scholar went on to describe how their faculty had failed to provide adequate office space and access to infrastructure essential to the project's success despite the fact that provision of both were conditions stipulated by the grant agreement.

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A third recent awardee would have been recruiting for and working full-time on two large grants that would have brought junior and senior researchers from nearly all continents to the university: many who attended a session she co-presented just before the reception had been awestruck by the architecture of her project. However, she left Oxford quietly in the weeks that followed.

Although I did not know it at the time, I too was to resign from the job I once would never have dreamed of giving up.

At a time of real or projected budget cuts, universities are sending staff regular reminders of the many schemes and often very large sums available for individual or collective research projects. This applies not only to science, engineering and the social sciences, but also to the humanities. Departments have hired research facilitators to keep staff informed about deadlines, local information sessions and funder events. They also help to design applications and calculate budgets according to need and opportunity.

For those who thrive on innovation and collaboration, these are the golden days. The opportunities provided to humanities scholars by the ERC and other European funders in particular are a source of envy among even those working in some of the most resource-rich universities in the world. Unsurprisingly, they have also raised the hopes and expectations of faculty administrators.

Applications for ERC schemes have risen consistently. Helga Nowotny, the council's president, recently attributed the large number of applications (700 for 15 awards) for its new synergy scheme, which awards sums of up to €15 million (?11.8 million) for a period of up to six years, in part to the despair of Italian institutions in desperate need of income. While despair may not have reached the same level across the UK, anecdotal evidence suggests that individual units and administrators are no less eager to maximise income from such schemes.

What are research projects for? I had long assumed that I had already answered this question in my 30-page application, but in the months following the ERC's "invitation to enter into an agreement", I returned to this question with greater urgency - and so too did many of the recent and past junior grant holders I met at the reception at Exeter College and at subsequent project manager events. For some this had something to do with the sudden realisation that managing a large grant imposes a weight of responsibility; for others the question surfaced time and again because their faculties had suddenly changed agreements that had been reached on investigator time, space, staffing and the use of research funds. In several cases, I learned, such agreements were changed more than once, to the detriment of the project and the well-being of the affected individuals. Some were diplomatic about their experiences, others less so.

One young man, a junior staff member, spoke very openly during a session on funding resources about "multiple fights" with his faculty as it revised his work schedule throughout the course of a three-year project, even into its critical closing months. Where does a junior or even mid-career academic turn when their faculty decides where the money goes? Grants such as these are owned in administrative terms by the university: in real terms that means they are controlled by faculties or departments, not principal investigators.

In my view, the money provided by external funders for particular projects should in the first place be used to serve the research goals outlined in the proposal. I also believe that any good research project serves, beyond experts in the relevant fields, the institution where it is housed primarily by embedding its activities in the work of colleagues and in pedagogical practice, thereby linking and strengthening research and teaching. This seems simple and uncontroversial, deceptively so. In reality, once the money has been won, faculties in many cases are not interested in the specifics of the research proposal. They zero in on the practical questions that may not have been considered when faculty committees evaluated the applications. A key technical issue when it comes to large multi-year grants concerns the amount of principal investigator time allocated to the project. Good advice for PIs? Full-time, 100 per cent commitment makes things a lot easier. I received this advice, but because I had been living in a small subject group with a very high turnover rate, I and the faculty agreed - or so I thought - that 70 per cent spread across five years would be a more feasible and fairer option. The 70 per cent salary cost paid for by the ERC was more than sufficient for a full-time replacement, and I could dedicate the remaining 30 per cent of my time to the most pressing teaching or administrative needs.

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But weeks before the final agreement with the ERC was due, my faculty presented me, by email, with a new timetable. The Humanities Division, it emerged, had determined on the basis of a typical workload model for all its academics that 40 per cent of staff time was already devoted to research. Given this, my faculty had decided that 40 per cent should be deducted from the PI time dedicated to my project. The percentages in the last column of the timetable showed what proportion of my time would remain for the project: 10 to 30 per cent, with the exception of one year of full-time leave.

How the 40 per cent was calculated I do not know: it most likely included evenings and weekends. It certainly did not match the actual workload of a university lecturer with a college fellowship. Would the revised timetable with which I was presented have met the rules established by the ERC? These require universities to ensure that the time it pays for is spent on the project.

Why would a researcher apply for a grant to fund research time she already has (in theory)? Suddenly the benefits of investing so much time and energy in a proposal - for which the odds of winning a grant are among the worst of all humanities schemes - became hard to see.

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The email captured two distinct philosophies of what research projects are for. One measures research and project management time at a rate sufficient to ensure that the work as described can be delivered. The other channels income from the project into unrelated departmental priorities.

ERC grants fund high-risk "frontier" research. Humanities scholars may want to have a separate discussion about what that means, but for most successful applicants I have encountered so far, it has meant them pushing themselves well beyond their comfort zone. In my grant application, I promised to work in comparative history and digital humanities, to investigate a large corpus of classical Chinese sources, and to coordinate the activities of a team of four researchers with different disciplinary backgrounds. The timetable I received in the email therefore amounted to a rip-off of the funder as well as the PI.

What lessons do I hope administrators and leaders in higher education will draw from all this? From the outset, universities should have clear criteria on how project time should be calculated and these should be shared with applicants, staff and administrators throughout the institution. These criteria should be adhered to throughout the entire project cycle.

Management must take an interest in the project, drop the cynicism and listen when an awardee explains the ways in which the research could benefit the teaching and operation of the faculty that houses it. If there are concerns about its impact, have open and timely conversations about how such projects can fit within the faculties that encourage their members to apply for funding. Do not drag resourcing decisions on for months, and do not present PIs with a new timetable weeks before the project's mandatory start date.

Consider the wider impact of a project on related faculties and research centres, support services, the morale of other applicants, the research environment throughout the university, and the internal and external reputation of faculties and colleges. The cost of seeking too much gain from large projects can be substantial.

For PIs, if the deal your faculty offers is unacceptable, be entrepreneurial and see whether you can find a better one elsewhere. The funder will most likely help you to do this and will extend deadlines if your concerns are valid. This will not solve all the problems, but you will be able to negotiate with your new employer from a position of strength. This year, two new awardees at Oxford, both young female members of staff in the humanities and social sciences, did just that. Another awardee left midway through his project. Others consulted for this article expressed a wish that they had done the same.

Oxford: most find us 'supportive'

Glenn Swafford, director of research services at the University of Oxford, says: "We regret that Hilde De Weerdt feels unhappy about her experiences when awarded a European Research Council grant at the University of Oxford. She was a valued colleague at Oxford from 2007 to 2012.

"As it is our policy to refrain from discussing individual cases publicly, we are not able to address many of the specific points in her article. We would, however, make some general remarks.

"Oxford has a large number of ERC grant holders and is pleased to have been able to help so many researchers secure these awards and manage their research projects. The vast majority of our researchers find the university to be a stimulating and supportive environment.

"ERC grants are portable. On some occasions people have moved from Oxford to other institutions; on other occasions, ERC grant holders have come to Oxford. Many universities offer special rewards (top-up funding, promise of tenure, etc) for anyone coming to them with an ERC grant, although this is not the practice at Oxford.

"The university's research committee continues to consider how we can ensure that all ERC grant holders have the best possible experience here at Oxford."

The ERC says that the portability of its grants is a "core principle" of its schemes. A grant is given ad personam to a researcher but administratively it is awarded to the host institution.

Its guidelines state that "grants are awarded to the host institution with the explicit commitment that this institution offers appropriate conditions for the principal investigator independently to direct the research and manage its funding for the duration of the project".

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An ERC spokeswoman says that about 120 grantees had requested to move host institution since 2007 after the signing of their grant agreements.