On Wednesday evening I stood in Parliament Square outside the Palace of Westminster, together with hundreds of other Christians who had come together to pray.

The last few months have seen our team at the Evangelical Alliance engage in the election with extraordinary energy and passion. Countless media interviews have been given. Tens, if not hundreds, of thousands of words have been written. We have supported and organised hundreds of hustings, spoken at many churches, conferences and festivals across the country and reached thousands with our popular election special of idea magazine which was so popular we had to order a reprint.

The 'Show Up' campaign, initiated by ourselves and Christians in Politics, amazingly drawing together more than 40 organisations, has raised the bar of Christian involvement. It has encouraged people not simply to go out to vote, but to engage even deeper with the strange and sometimes dirty world of politics.

So, as I stood in Parliament Square, just hours before the polling stations opened across the country, how did I pray? And what am I hoping for as the new government emerges?

I'm praying for good, stable government that is good for all – not just good for a few. A government that will remember the poor while protecting the economic wellbeing of many. I'll be praying for a government that will play its part as a member of the international community both in Europe and beyond, protecting and providing for those in the greatest need around the world. I'm praying for a government that will take seriously our responsibility as stewards of creation to care for the environment. I want a government that will allow us to live well as communities across the United Kingdom, despite our profound differences, enabling us to disagree respectfully. I'm praying for the accommodation of those who differ in religious belief, resulting in protection of religious liberty and freedom of expression. On top of all of this I'm praying that Christian MPs will be elected – women and men who will serve their constituencies and influence for good their parties and those in Westminster.

I'm sure I'm not alone in my prayers, and others will add to my list. I know Christians across the country are praying and so we should be. Not least because scripture exhorts us to this kind of prayer as a priority, Paul urging us: 'first of all, that petitions, prayers, intercession and thanksgiving be made for all people – for kings and all those in authority, that we may live peaceful and quiet lives in all godliness and holiness' (1 Tim 2:1-4).

But, and it's a big but, as a Christian I find myself in a complex relationship with those in power, even those who have been elected through a process in which I've participated. I'm required by scripture to respect, pray for, and even submit to those in authority. But I recognise that there is a higher authority, one to whom I have given my ultimate allegiance. My Saviour. My Lord. The declaration of Christians that has sounded loudly through the century makes it absolutely clear that Jesus is Lord, and this challenges all my earthly commitments. My submission to his lordship trumps everything. The lordship of Jesus does not simply extend to my religious or spiritual life; he is the Lord, the boss, the ultimate authority over all.

So as the election results unfold and the necessary negotiations to form a new government take place, I will continue to pray. Despite the political confusion that this election has highlighted, I will also affirm my trust in the one who is at work here on the earth, out-working His purposes, the one who will eventually be recognised by all, because the day will come when every knee will bow and every tongue will confess that Jesus is Lord.

Steve Clifford is general director of the Evangelical Alliance. Follow Steve on Twitter.